Author: A.A.Vagin
email: alexei@ysbl.york.ac.uk
Reference:
A. A. Vagin, G. N. Murshudov and B. V. Strokopytov
BLANC: the program suite for protein crystallography
J. Appl. Cryst. (1998). 31, 98 - 102
Atomic model represents X-ray crystal structure solution.
Complete description of this structure describes the crystall.
Hierarchy
First level of hierarchy of this description is the description of
the unit cell. It consists of the unit cell parameters and
space group symmetry name. The contents of the unit cell is generated
by the crystallographical symmetrical operators from the
contents of the asymmetrical part of unit cell.
Cell parameters, the list and the description of the links between
symm.related chains, Space group id and the cryst.symm. operators
define the crystal.
Second level describes the asymmetric part of unit cell.
The asymmetric part of the unit cell consists of the unit
structural elements - chains. The list of the chains and list of
links between the chains define the asymmetrical part of the unit cell.
Third level describes the chains. The description of chain is
the list of monomer, list of modifications and the descriptions
of these modifications, the list of links inside chain and
the descriptions of these links.
Fourth level describes the monomers. The description of monomer is
the list of atoms, the list of bonds, the list of angles and so on.
Fifth level describes the atoms. The atom's name, the atom's type,
the coordinates, B-factor, occupancy, multyplicity define the atom.
Definition
Chain /group/ - is numbered set of "monomers". The list of "monomers",
the links between monomers (for example: disulfide bridges, peptide bond),
the description of some modification of monomers (for example: terminus
of polypeptide chain) define the chain. The polymer (lenear or not as
sugar) is covalet bonded set of monomers - chain. A set of water molecule
is a chain. Chain may contain only one monomer.
Monomer /residue/ - is a set of atoms connected by bonds, or a single
atom.
Coordinate file
Coordinate file contains the information which dependent on the
conformation of the molecule (coordinates, occupancy, B-factors)
B-factors) and the list of modifications to and links between
actual monomers. The information about the names of chains and
monomers, and the serial numbers of monomers for the links must
be present in the CIFile. Link's ID, modification's ID, names of
chains, monomers, atoms are the pointers to the chemical description
in the dictionary.
Dictionary
Dictionary contains information about:
1. the chemical structure of the monomers (atom's types,
bond's lengths, angles, chirality, planarity),
2. the tree like structure of each monomer,
3. chemical structure of links between monomers (peptide bond,
disulfide bridges,...),
4. chemical details of the modifications of monomers (e.g. termini of
polypeptide chains,...)
5. energetic parameters.
Some monomer has "minimal description : list of atom, atom's types
and bonds. Complete description can be derived from minimal.
Structure/Restraint files
Coordinate file and Dictionary describe structure completely.
But there are a lot of data in the dictionary which is not
concern this particular structure. Makecif creates two files
with necessary information from Dictionary:
1. structure file with
chemical atom's types, WDV and ion radii,
tree like structure description
2. restrain file with
description of bonds, angles, tortions, chiralities,
planarities
Read PDB file
Reading PDB file Makecif uses from PDB file only folowing records:
HEADER COMPND CRYST1 SCALE HETATM TER
SSBOND MODRES LINK CISPEP ATOM ANISOU
a) atom name correction and element definition, if this is absent
in input file.
Program changes PDB style of H atom's name to human style.
For example : 1HN1 --> HN11
Accoding PDB convention program change character ' (quota) to * (star)
in atom's name of DNA/RNA.
C-terminus atom O of polipeptide 'OT ' --> 'OXT ',
AND for DNA/RNA:
'OXT ' --> 'O3T '
'O3G ' --> 'O3T '
'O3P ' --> 'O3T '
Atom O for water must has name 'O '
If there is character ' (quota) in atom's name program changes
it to , (comma)
b) check and correction residue name,
residue type definition.
If there is character ' (quota) in residue's name program changes
it to , (comma)
Program changes residue's name of DNA/RNA:
CYT --> C
ADE --> A
THY --> T
GUA --> G
URI --> U
c) chain correction,check chain connection
d) read links and modification
Check monomers
Program checks a presence of description of monomers and defines
type of monomers.
There are following monomer's types:
non-polymer
peptide
polymer
DNA/RNA
pyranose
solvent
Peptides (L and D peptides) are:
'CYS','SER','THR','PRO','ALA','GLY','ASN','ASP'
,'GLU','GLN','HIS','ARG','LYS','MET','ILE','LEU'
,'VAL','PHE','TYR','TRP','TRY','PRZ','PR0','ILU'
,'CYX','CSS','CSH','CYH','ASX','GLX','ACD','INI'
,'ABU','ALB','ALI','ARO','BAS','HYP','PCA','SAR'
,'ABA','BMT','MLE','MVA','DVA','MSE','PTR','DAL'
,'NLE','BLE','B1F','B2F','B2A','B2I','B2V','DPR'
,'DPN','DTR','DTH','TYS','CGU','ANT','ILG','OCS'
,'KCX','SAH','SAM','SEP','LLP','5HP','CSO','ORN'
Polymers are:
'STA','DFO','FOR','BOC','IVA','NME','ACE','DAM'
,'ETA','ANI','ADD','ACB','TFA','DIP','MPR','CXM','BAL'
DNA/RNA are:
'A ','C ','G ','T ','U ','I ','+A ','+C '
,'+G ','+T ','+U ','1MA','1MG','2MG','5MC','5MU'
,'7MG','H2U','M2G','OMC','OMG','OMU','PSU','YG '
Pyranoses are:
'MAN','NAG','FUC','GAL','GLC','GCU','CEG','XYS'
,'ARB','RIP','ABE','RAM','MAG','MMA','GSA'
Scheme of the check of the presence of description of monomers.
Global search is an algorithm to matching two description.
Make_new means to create new complete description.
+------------------------------------+
! Look at the name in the dictionary !
! Is that in the dictionary ? !
+------------------------------------+
! !
no ! ! yes
v v
+---------------+ +----------------------+
+-->-! Global search ! yes ! Minimal description !
! ! matching ? !--->----! ? !
! +---------------+ +----------------------+
! ! ! !
! no ! ! yes ! no
! ! ! v
! v v +----------------------+
^ ! ! ! is this polipeptide, !
! ! ! ! DNA/RNA, sugar ? !
! ! ! +----------------------+
! ! ! ! !
! ! ! ! no ! yes
! ! ! v v
! ! no ! +----------------+ !
+---<----------------<------------- ! Completeness ? ! !
! ! +----------------+ !
v v ! !
! ! ! yes !
! ! ! !
+-----------------------+ v v
! Make_new ! ! !
+-----------------------+ ! !
! ! !
! ! !
v v v
Check structure description
1. check of atoms in special position.
2. check of chain connectivity and definition of connection types.
Only peptides, polymers , DNA/RNA and pyranos can form chain.
There are following connection types, which can form chain:
for peptides, polymers:
'TRANS '
'CIS '
'PTRANS '
'PCIS '
'FOR_C-N '
'FOR_C-C '
'ACE_C-N '
'DFO_C-N '
'NME_N-C '
'IVA_C-N '
'BOC_C-N '
'DFO_N-C '
'STA_C-N '
'STA_N-C '
for DNA/RNA:
'p '
for pyranoses:
'BETA1-2 '
'BETA1-3 '
'BETA1-4 '
'BETA1-6 '
'ALPHA1-2'
'ALPHA1-3'
'ALPHA1-4'
'ALPHA1-6'
3. check of inter/intra chain links
if description of link there is not in the dictionary, program
can create it.
4. check and create new list of chains and set type of terminus residues.
Chain types:
'non-polymer'
'polypeptide'
'DNA/RNA '
'saccharide'
'water '
Terminus IDs:
initial:
'NH3 '
'FOR-N '
'p5*END '
'5*END '
'NH3-COO '
'TERMINUS'
final:
'COO '
'FOR-C '
'p3*END '
'3*END '
'NH3-COO '
'TERMINUS'
'CM-COO '
5. check completeness of atom's list of residue.
Finally program create list of restraints or rebuilds missing atoms.
Rebuilding
Program rebuilds missing atoms used information from
monomer's library.
Restraints
Program writes to output file ideal values of reatraints and
its observed values. If output file is formatted file
( keyword FORM = F ) it is possible to look at and check.
mon_lib_com.cif - description links and modifications
mon_lib_prot.cif - amino-acids
mon_lib_na.cif - DNA/RNA
mon_lib_sug.cif - sugars
mon_lib_met.cif - metals
mon_lib_1.cif - small molecules
mon_lib_2.cif - - - - - -
. . . . . . . .
ener_lib.cif, - energetic parameters
Program can read additional library of monomers.
1. with atomic coordinates, symmetry and unit cell
parameters. / file extension "crd"/
2. with chemical structure description and atomic
scattering structure factors. / file extension "str"/
3. with restraints: standard values of bonds, angles,
torsion angles, chirality centres, plan groups, its
actual values in the structure. / file extension "rst"/
4. with Van-der-Waals and H_bond restraints: standard values
of distanceis and its actual values in the structure. /file
extension "vdw"/
To get started with MAKECIF, you first have to answer two questions:
1) Do you want to have FILE-DOCUMENT /makecif.doc/ ? /<N>/Y/A :
N - means without DOC-file
Y - with new contents
A - means to keep old contents and add new information
with DOC-file program creates batch file: makecif.bat
DOC Y
2) input-coord-file
FILE_C t.pdb
After that you can use akeywords in any order, if you want to use.
Keywords:
FILE_O <new> - output_CIFiles /name without extention/
default name: 'new'
output files will be:
new.crd
new.str
new.rst
new.vdw
new_XXX.ps
new.lib
FILE_L < > - additional library, " " means without this file
SPEC <N>/Y - Y - check atoms in special position, N - not use it.
DMIN <0.5> - minimal distance to recognize atom in special position
CONN <N>/Y/D - N - only check chain"s connection between residues.
Y - use new chain"s connection between residues.
D - use new but ignore user"s definition
CIS <N>/Y - Y - check and change peptide link
SS <Y>/N/D - N - only check SS-links
Y - use new SS-links between residues.
D - use new but ignore user"s definition
SUGAR <N>/Y/D - N - only check links between residues.
Y - use new links between residues.
D - use new but ignore user"s definition
LINK <N>/Y/D - N - only check links between residues.
Y - use new links between residues.
D - use new but ignore user"s definition
CHAIN <N>/Y - Y - check and change chain description
PEPT <N>/Y - Y - check and correct AA in PDB file (L or D)
SYMM <N>/Y - Y - use links between symmetry reated residues.
CHECK <N>/Y - Y - full check of all monomers
CUT <0> - distance cut_off, 0 - means without VDW and H-bond
restraints
HFLAG <Y>/A/N - Y - hydrogen atoms where they are (not create new)
A - with all hydrogen atoms (rebuild all missing H atoms)
N - without hydrogen atoms (i.e. remove H)
RFLAG <N>/Y - Y - rebuild non-hydrogen atoms
restraints will not be created if HFLAG="A" or RFLAG="Y"
FORM <F>/U - format of restrain file, U - unformatted
NOSG <0> - Number of new space group
CELL <0> - new cell: A,B,C,Alpha,Beta,Gamma
LIST <M>/S/L - S short output, L - long, M - medium
LOUT <new.lib> - output file of new dictionary
- library manager.
reads library of monomers, gives information about some
monomer, creates PostScript file with picture and information
about bonds, angles, ...
can read additional library, add two libraries and write to
a new library file ;
can create description of new monomer reading coordinates
from PDB file of CIFile.
- restrain checker.
reads CIFiles of coordinates and restraints,
gives information about restraints (to DOC_file),
writes PDB_file or/and CIFile of coordinates.
- energy minimization / or B_factor regularization /
minimizes the energy of structure using the restraints files
from program MAKECIF.
E_total = E_bond + E_angle + E_tors + E_vdw + E_hb
E_bond = Sum ( Kb * (Bobs -Bidl)**2 )
E_angle = Sum ( Ka * (ANGLEobs -ANGLEidl)**2)
E_tors = Sum ( Kt * (PHIobs -PHIidl)**2 )
E_vdw = Lennard-Jones 6-12 potential
E_bond = 10-12 potential
Copy file makecif.tar.gz
and uncompress it (`gunzip makecif.tar.gz')
After untaring `makecif.tar' ( command: tar xvf makecif.tar ),
you will get a makecif directory with src, dic, and bin subdirectories
and README file.
To build the executable, go in src subdirectory.
Define compiler: setenv BLANC_FORT
for example:
for linux and mac:
setenv BLANC_FORT "f77 -fno-globals -fno-automatic -O1 -w"
for linux intel compiler:
setenv BLANC_FORT "ifort -static -O1"
for mac ibm compiler:
setenv BLANC_FORT " xlf -qextname -qarch=auto -qtune=auto -qstrict -O3"
else
setenv BLANC_FORT "f77 -O1"
1. `make makecif_all', the executable (makecif) will finish up in the bin
directory; providing the full pathname (.../makecif/bin/makecif) one
can execute it from anywhere without having to define and environmental
variable.
2. `make libcheck_all' for libcheck program
3. `make modcheck_all' for modcheck program
4. `make emin_all' for emin program
CRYST1
This record defines cell dimensions and space group symmetry
corresponding to this crystal.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION
-------------------------------------------------------------
1 - 6 Record name "CRYST1"
7 - 15 Real(9.3) a a (Angstroms).
16 - 24 Real(9.3) b b (Angstroms).
25 - 33 Real(9.3) c c (Angstroms).
34 - 40 Real(7.2) alpha alpha (degrees).
41 - 47 Real(7.2) beta beta (degrees).
48 - 54 Real(7.2) gamma gamma (degrees).
56 - 66 LString sGroup Space group.
Details
The Hermann-Mauguin space group symbol is given without parentheses,e.g.
P 43 21 2. Please note that the screw axis is described as a two
digit number.
The full international Hermann-Mauguin symbol is used,e.g. P 1 21 1 instead
of P 21.
For a rhombohedral space group in the hexagonal setting, the lattice
type symbol used is H.
Example:
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890123456789
CRYST1 76.560 55.400 84.650 90.00 116.53 90.00 P 1 21 1
SCALEn
The SCALEn (n = 1, 2, or 3) records present the transformation from the
orthogonal coordinates as contained in the entry to fractional
crystallographic coordinates.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION
----------------------------------------------------------------
1 - 6 Record name "SCALEn" n=1, 2, or 3
11 - 20 Real(10.6) s[n][1] Sn1
21 - 30 Real(10.6) s[n][2] Sn2
31 - 40 Real(10.6) s[n][3] Sn3
46 - 55 Real(10.5) u[n] Un
Details
The standard orthogonal Angstroms coordinate system used by the PDB is
related to the axial system of the unit cell supplied (CRYST1 record) by the
following definition:
If vector a, vector b, vector c describe the crystallographic cell edges, and
vector A, vector B, vector C are unit cell vectors in the default orthogonal
Angstroms system, then vector A, vector B, vector C and vector a, vector b,
vector c have the same origin; vector A is parallel to vector a, vector B is
parallel to vector C times vector A, and vector C is parallel to vector a
times vector b (i.e. vector c*).
If the orthogonal Angstroms coordinates are X, Y, Z, and the fractional cell
coordinates are xfrac, yfrac, zfrac, then:
xfrac = S11X + S12Y + S13Z + U1
yfrac = S21X + S22Y + S23Z + U2
zfrac = S31X + S32Y + S33Z + U3
For NMR, fiber diffraction - fiber sample, and theoretical model entries,
SCALE is given as an identity matrix with no translation.
SSBOND
The SSBOND record identifies each disulfide bond in protein and polypeptide
structures by identifying the two residues involved in the bond.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION
----------------------------------------------------------------------------
1 - 6 Record name "SSBOND"
8 - 10 Integer serNum Serial number.
12 - 14 LString(3) "CYS" Residue name.
16 Character chainID1 Chain identifier.
18 - 21 Integer seqNum1 Residue sequence number.
22 AChar icode1 Insertion code.
26 - 28 LString(3) "CYS" Residue name.
30 Character chainID2 Chain identifier.
32 - 35 Integer seqNum2 Residue sequence number.
36 AChar icode2 Insertion code.
60 - 65 SymOP sym1 Symmetry operator for 1st residue.
67 - 72 SymOP sym2 Symmetry operator for 2nd residue.
Example:
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890123456789
SSBOND 1 CYS E 48 CYS E 51 2555
Details
Bond distances between the sulfur atoms must be close to expected values.
The cysteine closer to the N-terminal is listed first in each intra-chain
pair.
The cysteine which occurs first in the coordinate entry is listed first for
inter-chain pairs.
sym1 and sym2 are given as blank when the identity operator (and no cell
translation) is to be applied to the residue.
LINK
The LINK records specify connectivity between residues that is not implied by
the primary structure. Connectivity is expressed in terms of the atom names.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION
-----------------------------------------------------------------------------
1 - 6 Record name "LINK "
13 - 16 Atom name1 Atom name.
17 Character altLoc1 Alternate location indicator.
18 - 20 Residue name resName1 Residue name.
22 Character chainID1 Chain identifier.
23 - 26 Integer resSeq1 Residue sequence number.
27 AChar iCode1 Insertion code.
30 - 40 Real Distance Distance between atoms if
not defined in the dictionary
(F10.5)
43 - 46 Atom name2 Atom name.
47 Character altLoc2 Alternate location indicator.
48 - 50 Residue name resName2 Residue name.
52 Character chainID2 Chain identifier.
53 - 56 Integer resSeq2 Residue sequence number.
57 AChar iCode2 Insertion code.
60 - 65 SymOP sym1 Symmetry operator for 1st atom.
67 - 72 SymOP sym2 Symmetry operator for 2nd atom.
73 - 80 LinkID name1 Reference to link described
in the dictionary
Example:
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890123456789
LINK MN MN 391 OE2 GLU 217 2565
Details
The atoms involved in bonds between HET groups or between a HET group
and standard residue are listed.
Interresidue linkages not implied by the primary structure are listed
e.g.reduced peptide bond).
Non-standard linkages between residues, e.g.side-chain to side-chain, are
listed.
Each LINK record specifies one linkage.
sym1 and sym2 are given as blank when the identity operator (and no cell
translation) is to be applied to the atom.
Note that Distance and LinkID columns are not in pdb definition. They are
specific to refmac and makecif
CISPEP
CISPEP records specify the prolines and other peptides found to be in the
cis conformation.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION
-------------------------------------------------------------------------
1 - 6 Record name "CISPEP"
8 - 10 Integer serNum Record serial number.
12 - 14 LString(3) pep1 Residue name.
16 Character chainID1 Chain identifier.
18 - 21 Integer seqNum1 Residue sequence number.
22 AChar icode1 Insertion code.
26 - 28 LString(3) pep2 Residue name.
30 Character chainID2 Chain identifier.
32 - 35 Integer seqNum2 Residue sequence number.
36 AChar icode2 Insertion code.
44 - 46 Integer modNum Identifies the specific model.
54 - 59 Real(6.2) measure Measure of the angle in
degrees.
Example:
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890123456789
SSBOND 1 CYS E 48 CYS E 51 2555
ATOM
The ATOM records present the atomic coordinates for standard residues. They
also present the occupancy and temperature factor for each atom. Heterogen
coordinates use the HETATM record type. The element symbol is always
present on each ATOM record; segment identifier and charge are optional.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION
---------------------------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer serial Atom serial number.
13 - 16 Atom name Atom name.
17 Character altLoc Alternate location indicator.
18 - 20 Residue name resName Residue name.
22 Character chainID Chain identifier.
23 - 26 Integer resSeq Residue sequence number.
27 AChar iCode Code for insertion of residues.
31 - 38 Real(8.3) x Orthogonal coordinates for X in
Angstroms.
39 - 46 Real(8.3) y Orthogonal coordinates for Y in
Angstroms.
47 - 54 Real(8.3) z Orthogonal coordinates for Z in
Angstroms.
55 - 60 Real(6.2) occupancy Occupancy.
61 - 66 Real(6.2) tempFactor Temperature factor.
73 - 76 LString(4) segID Segment identifier,left-justified.
77 - 78 LString(2) element Element symbol, right-justified.
79 - 80 LString(2) charge Charge on the atom.
Details
ATOM records for proteins are listed from amino to carboxyl terminus.
Nucleic acid residues are listed from the 5' to the 3' terminus.
No ordering is specified for polysaccharides.
The list of ATOM records in a chain is terminated by a TER record.
If more than one model is present in the entry, each model is delimited by
MODEL and ENDMDL records.
If an atom is provided in more than one position, then a non-blank alternate
location indicator must be used as the alternate location indicator
for each of the positions. Within a residue all atoms that are associated
with each other in a given conformation are assigned the same alternate
position indicator.
ANISOU
The ANISOU records present the anisotropic temperature factors.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION
----------------------------------------------------------------------
1 - 6 Record name "ANISOU"
7 - 11 Integer serial Atom serial number.
13 - 16 Atom name Atom name.
17 Character altLoc Alternate location
indicator.
18 - 20 Residue name resName Residue name.
22 Character chainID Chain identifier.
23 - 26 Integer resSeq Residue sequence number.
27 AChar iCode Insertion code.
29 - 35 Integer u[0][0] U(1,1)
36 - 42 Integer u[1][1] U(2,2)
43 - 49 Integer u[2][2] U(3,3)
50 - 56 Integer u[0][1] U(1,2)
57 - 63 Integer u[0][2] U(1,3)
64 - 70 Integer u[1][2] U(2,3)
73 - 76 LString(4) segID Segment identifier,left-justified.
77 - 78 LString(2) element Element symbol,right-justified.
79 - 80 LString(2) charge Charge on the atom.
Details
Columns 7 - 27 and 73 - 80 are identical to the corresponding
ATOM/HETATM record.
The anisotropic temperature factors (columns 29 - 70) are scaled by a factor
of 10**4 (Angstroms**2) and are presented as integers.
The anisotropic temperature factors are stored in the same coordinate frame as
the atomic coordinate records.
MODRES
MODRES is mainly used to avoid 3 letter limitation of the pdb residue names.
Using this record one can change residue names for longer name (maximum 8
character) which is present in the dictionary file. It could also be used for
any other modifications described in the dictionary.
Example:
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890123456789
MODRES DTT A 950 DTT_oxd RENAME
It means that residue number 950 of chain A is DTT in pdb but it should be
interpreted as DTT_oxd which is present in dictionary (either supplied by us
or created by user).
Note that as all pdb records it is formatted also. Maximum length for
renamed residue is 8 characters.
TER
termination record.
# -------------------------------- makecif <<stop # -------------------------------- # first line : "_DOC <N>,Y,A " # N - means without DOC-file: "makecif.doc" # Y - create new file or rewrite if it is old file # A - means to keep old contents and add new information # _DOC Y # # input-coord-file _FILE_C input.pdb # # Keywords: # _spec Y _END stop
HEADER HYDROLASE (ENDORIBONUCLEASE) 13-DEC-90 2SAR COMPND RIBONUCLEASE SA (E.C.3.1.4.8) COMPLEX WITH 3*-*GUANYLIC ACID LINK LEU A 8 . THR A 95 gap SSBOND 1 CYS A 7 CYS A 96 CRYST1 64.900 78.320 38.790 90.00 90.00 90.00 P 21 21 21 SCALE1 0.015410 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012770 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025780 0.00000 ATOM 1 N GLY A 4 49.878 12.391 1.471 1.00 22.84 N ATOM 2 CA GLY A 4 50.392 12.195 0.095 1.00 21.44 C ATOM 3 C GLY A 4 51.497 11.105 0.311 1.00 19.35 C ATOM 4 O GLY A 4 51.732 10.714 1.491 1.00 20.07 O ATOM 5 N THR A 5 51.943 10.633 -0.833 1.00 18.80 N ATOM 6 CA THR A 5 52.978 9.591 -1.068 1.00 18.48 C ATOM 7 CB THR A 5 52.579 8.524 -2.141 1.00 21.50 C ATOM 8 OG1 THR A 5 51.306 7.990 -1.553 1.00 28.23 O ATOM 9 CG2 THR A 5 53.417 7.313 -2.468 1.00 22.70 C ATOM 10 C THR A 5 54.245 10.338 -1.481 1.00 19.87 C ATOM 11 O THR A 5 54.107 11.414 -2.140 1.00 22.07 O ATOM 12 N VAL A 6 55.411 9.885 -1.065 1.00 14.29 N ATOM 13 CA VAL A 6 56.674 10.584 -1.455 1.00 11.27 C ATOM 14 CB VAL A 6 57.267 11.521 -0.387 1.00 14.08 C ATOM 15 CG1 VAL A 6 57.506 10.835 0.953 1.00 13.75 C ATOM 16 CG2 VAL A 6 58.601 12.152 -0.891 1.00 14.03 C ATOM 17 C VAL A 6 57.604 9.394 -1.863 1.00 9.96 C ATOM 18 O VAL A 6 57.589 8.352 -1.143 1.00 10.60 O ATOM 19 N CYS A 7 58.299 9.593 -2.933 1.00 9.43 N ATOM 20 CA CYS A 7 59.230 8.491 -3.295 1.00 8.16 C ATOM 21 CB CYS A 7 59.862 8.875 -4.600 1.00 11.22 C ATOM 22 SG CYS A 7 58.674 8.605 -5.948 1.00 13.06 S ATOM 23 C CYS A 7 60.328 8.445 -2.226 1.00 8.81 C ATOM 24 O CYS A 7 60.665 9.500 -1.695 1.00 12.60 O ATOM 25 N LEU A 8 60.830 7.282 -1.929 1.00 10.42 N ATOM 26 CA LEU A 8 61.948 7.038 -1.028 1.00 8.80 C ATOM 27 CB LEU A 8 62.273 5.519 -1.032 1.00 6.35 C ATOM 31 C LEU A 8 63.189 7.895 -1.465 1.00 12.21 C ATOM 32 O LEU A 8 63.958 8.546 -0.697 1.00 12.18 O ATOM 33 N THR A 95 59.269 2.156 -4.288 1.00 11.37 N ATOM 34 CA THR A 95 59.482 1.757 -5.679 1.00 11.20 C ATOM 35 CB THR A 95 58.110 1.160 -6.309 1.00 12.23 C ATOM 36 OG1 THR A 95 57.309 2.337 -6.623 1.00 15.52 O ATOM 37 CG2 THR A 95 57.400 0.169 -5.394 1.00 8.57 C ATOM 38 C THR A 95 60.088 2.925 -6.450 1.00 11.28 C ATOM 39 O THR A 95 60.392 2.774 -7.657 1.00 15.06 O ATOM 40 N CYS A 96 60.305 4.121 -5.923 1.00 10.25 N ATOM 41 CA CYS A 96 60.824 5.246 -6.657 1.00 12.91 C ATOM 42 CB CYS A 96 59.596 5.973 -7.309 1.00 12.80 C ATOM 43 SG CYS A 96 58.398 6.673 -6.122 1.00 11.60 S ATOM 44 C CYS A 96 61.741 6.176 -5.847 1.00 12.25 C ATOM 45 O CYS A 96 61.895 5.916 -4.665 1.00 11.30 O ATOM 46 OXT CYS A 96 62.238 7.178 -6.423 1.00 12.45 O ATOM 47 S SO4 A 97 70.061 18.967 18.614 1.00 22.88 S ATOM 48 O1 SO4 A 97 69.463 17.644 18.723 1.00 21.16 O ATOM 49 O2 SO4 A 97 69.709 19.567 17.315 1.00 21.21 O ATOM 50 O3 SO4 A 97 71.566 19.061 18.507 1.00 20.80 O ATOM 51 O4 SO4 A 97 69.750 20.041 19.660 1.00 24.52 O ATOM 52 O HOH X 215 56.967 2.009 2.365 1.00 16.42 O ATOM 53 O HOH X 216 54.165 2.368 0.478 1.00 31.00 O ATOM 54 O HOH X 217 54.400 7.181 -5.723 1.00 35.24 O ATOM 55 O HOH X 218 63.721 0.084 0.107 1.00 24.55 O ATOM 56 O HOH X 219 56.259 2.010 -9.042 1.00 31.18 O ATOM 57 O HOH X 220 64.250 5.840 -8.328 1.00 42.84 O ATOM 58 O HOH X 221 60.213 10.112 24.687 1.00 28.17 O ATOM 59 O HOH X 222 62.790 13.500 20.557 1.00 28.93 O
Coordinate file: new.crd
data_structure_2SAR
_entry.id 2SAR
_database_2.code_PDB 2SAR
_struct_keywords.text 'HYDROLASE (ENDORIBONUCLEASE)'
_struct.title 'RIBONUCLEASE SA (E.C.3.1.4.8) COMPLEX WITH 3*-*GUANYLIC ACID '
_audit.creation_date 1990-12-13
_software.name blanc
############
## ENTITY ##
############
loop_
_entity.id
_entity.type
AA polypeptide
SO4 non-polymer
HOH water
#####################
## ENTITY_POLY_SEQ ##
#####################
loop_
_entity_poly_seq.mon_id
_entity_poly_seq.ccp4_auth_seq_id
_entity_poly_seq.entity_id
_entity_poly_seq.ccp4_back_connect_type
_entity_poly_seq.ccp4_num_mon_back
_entity_poly_seq.ccp4_mod_id
#
GLY 4 AA . n/a NH3
THR 5 AA TRANS 4 .
VAL 6 AA TRANS 5 .
CYS 7 AA TRANS 6 .
LEU 8 AA TRANS 7 .
THR 95 AA gap 8 .
CYS 96 AA TRANS 95 COO
#################
## ENTITY_LINK ##
#################
loop_
_entity_link.ccp4_link_id
_entity_link.ccp4_entity_id
_entity_link.ccp4_comp_id_1
_entity_link.ccp4_auth_seq_id_1
_entity_link.ccp4_atom_id_1
_entity_link.ccp4_comp_id_2
_entity_link.ccp4_auth_seq_id_2
_entity_link.ccp4_atom_id_2
_entity_link.dist
SS AA CYS 7 SG CYS 96 SG .
##########
## CELL ##
##########
_cell.entry 2SAR
_cell.length_a 64.900
_cell.length_b 78.320
_cell.length_c 38.790
_cell.angle_alpha 90.000
_cell.angle_beta 90.000
_cell.angle_gamma 90.000
##############################
## FRACTIONALISATION MATRIX ##
##############################
_atom_sites.fract_transf_matrix[1][1] 0.015410
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] 0.000000
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 0.012770
_atom_sites.fract_transf_matrix[2][3] 0.000000
_atom_sites.fract_transf_matrix[3][1] 0.000000
_atom_sites.fract_transf_matrix[3][2] 0.000000
_atom_sites.fract_transf_matrix[3][3] 0.025780
_atom_sites.fract_transf_vector[1] 0.000000
_atom_sites.fract_transf_vector[2] 0.000000
_atom_sites.fract_transf_vector[3] 0.000000
##############
## SYMMETRY ##
##############
_symmetry.entry.id 2SAR
_symmetry.space_group_name_H-M 'P 21 21 21'
_symmetry.Int_Tables_number 19
loop_
_symmetry_equiv.id
_symmetry_equiv.pos_as_xyz
1 +X,+Y,+Z,
2 1/2-X,-Y,1/2+Z,
3 -X,1/2+Y,1/2-Z,
4 1/2+X,1/2-Y,-Z,
#################
## STRUCT_ASYM ##
#################
loop_
_struct_asym.id
_struct_asym.entity_id
AA AA
Aa SO4
XX HOH
###############
## ATOM_SITE ##
###############
loop_
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.auth_seq_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.type_symbol
_atom_site.calc_flag
1 N . GLY AA 4 49.878 12.391 1.471 1.00 22.84 N .
2 CA . GLY AA 4 50.392 12.195 0.095 1.00 21.44 C .
3 C . GLY AA 4 51.497 11.105 0.311 1.00 19.35 C .
4 O . GLY AA 4 51.732 10.714 1.491 1.00 20.07 O .
5 N . THR AA 5 51.943 10.633 -0.833 1.00 18.80 N .
6 CA . THR AA 5 52.978 9.591 -1.068 1.00 18.48 C .
7 CB . THR AA 5 52.579 8.524 -2.141 1.00 21.50 C .
8 OG1 . THR AA 5 51.306 7.990 -1.553 1.00 28.23 O .
9 CG2 . THR AA 5 53.417 7.313 -2.468 1.00 22.70 C .
10 C . THR AA 5 54.245 10.338 -1.481 1.00 19.87 C .
11 O . THR AA 5 54.107 11.414 -2.140 1.00 22.07 O .
12 N . VAL AA 6 55.411 9.885 -1.065 1.00 14.29 N .
13 CA . VAL AA 6 56.674 10.584 -1.455 1.00 11.27 C .
14 CB . VAL AA 6 57.267 11.521 -0.387 1.00 14.08 C .
15 CG1 . VAL AA 6 57.506 10.835 0.953 1.00 13.75 C .
16 CG2 . VAL AA 6 58.601 12.152 -0.891 1.00 14.03 C .
17 C . VAL AA 6 57.604 9.394 -1.863 1.00 9.96 C .
18 O . VAL AA 6 57.589 8.352 -1.143 1.00 10.60 O .
19 N . CYS AA 7 58.299 9.593 -2.933 1.00 9.43 N .
20 CA . CYS AA 7 59.230 8.491 -3.295 1.00 8.16 C .
21 CB . CYS AA 7 59.862 8.875 -4.600 1.00 11.22 C .
22 SG . CYS AA 7 58.674 8.605 -5.948 1.00 13.06 S .
23 C . CYS AA 7 60.328 8.445 -2.226 1.00 8.81 C .
24 O . CYS AA 7 60.665 9.500 -1.695 1.00 12.60 O .
25 N . LEU AA 8 60.830 7.282 -1.929 1.00 10.42 N .
26 CA . LEU AA 8 61.948 7.038 -1.028 1.00 8.80 C .
27 CB . LEU AA 8 62.273 5.519 -1.032 1.00 6.35 C .
28 CG . LEU AA 8 0.000 0.000 0.000 0.00 0.00 C M
29 CD1 . LEU AA 8 0.000 0.000 0.000 0.00 0.00 C M
30 CD2 . LEU AA 8 0.000 0.000 0.000 0.00 0.00 C M
31 C . LEU AA 8 63.189 7.895 -1.465 1.00 12.21 C .
32 O . LEU AA 8 63.958 8.546 -0.697 1.00 12.18 O .
33 N . THR AA 95 59.269 2.156 -4.288 1.00 11.37 N .
34 CA . THR AA 95 59.482 1.757 -5.679 1.00 11.20 C .
35 CB . THR AA 95 58.110 1.160 -6.309 1.00 12.23 C .
36 OG1 . THR AA 95 57.309 2.337 -6.623 1.00 15.52 O .
37 CG2 . THR AA 95 57.400 0.169 -5.394 1.00 8.57 C .
38 C . THR AA 95 60.088 2.925 -6.450 1.00 11.28 C .
39 O . THR AA 95 60.392 2.774 -7.657 1.00 15.06 O .
40 N . CYS AA 96 60.305 4.121 -5.923 1.00 10.25 N .
41 CA . CYS AA 96 60.824 5.246 -6.657 1.00 12.91 C .
42 CB . CYS AA 96 59.596 5.973 -7.309 1.00 12.80 C .
43 SG . CYS AA 96 58.398 6.673 -6.122 1.00 11.60 S .
44 C . CYS AA 96 61.741 6.176 -5.847 1.00 12.25 C .
45 O . CYS AA 96 61.895 5.916 -4.665 1.00 11.30 O .
46 OXT . CYS AA 96 62.238 7.178 -6.423 1.00 12.45 O .
47 S . SO4 Aa 97 70.061 18.967 18.614 1.00 22.88 S .
48 O1 . SO4 Aa 97 69.463 17.644 18.723 1.00 21.16 O .
49 O2 . SO4 Aa 97 69.709 19.567 17.315 1.00 21.21 O .
50 O3 . SO4 Aa 97 71.566 19.061 18.507 1.00 20.80 O .
51 O4 . SO4 Aa 97 69.750 20.041 19.660 1.00 24.52 O .
52 O . HOH XX 215 56.967 2.009 2.365 1.00 16.42 O .
53 O . HOH XX 216 54.165 2.368 0.478 1.00 31.00 O .
54 O . HOH XX 217 54.400 7.181 -5.723 1.00 35.24 O .
55 O . HOH XX 218 63.721 0.084 0.107 1.00 24.55 O .
56 O . HOH XX 219 56.259 2.010 -9.042 1.00 31.18 O .
57 O . HOH XX 220 64.250 5.840 -8.328 1.00 42.84 O .
58 O . HOH XX 221 60.213 10.112 24.687 1.00 28.17 O .
59 O . HOH XX 222 62.790 13.500 20.557 1.00 28.93 O .
Chemical structure file: new.str
global_
_entry.id 2SAR
_audit.creation_date 13-DEC-90
_struct.title 'RIBONUCLEASE SA (E.C.3.1.4.8) COMPLEX WITH 3*-*GUANYLIC AC'
#
data_struct_list
loop_
_atom_type.symbol
_atom_type.scat_Cromer_Mann_a1
_atom_type.scat_Cromer_Mann_a2
_atom_type.scat_Cromer_Mann_a3
_atom_type.scat_Cromer_Mann_a4
_atom_type.scat_Cromer_Mann_b1
_atom_type.scat_Cromer_Mann_b2
_atom_type.scat_Cromer_Mann_b3
_atom_type.scat_Cromer_Mann_b4
_atom_type.scat_Cromer_Mann_c
_atom_type.scat_dispersion_real
_atom_type.scat_dispersion_imag
_atom_type.radius_contact
N 12.21260 3.13220 2.01250 1.16630
0.00570 9.89330 28.99750 0.58260
-11.52900 0.02900 0.01800 0.00000
C 2.31000 1.02000 1.58860 0.86500
20.84390 10.20750 0.56870 51.65120
0.21560 0.01700 0.00900 0.00000
O 3.04850 2.28680 1.54630 0.86700
13.27710 5.70110 0.32390 32.90890
0.25080 0.04700 0.03200 0.00000
S 6.29150 3.03530 1.98910 1.54100
2.43860 32.33370 0.67850 81.69370
1.14070 0.24400 0.33000 0.00000
loop_
_struct_atom.serial_number
_struct_atom.chem_type
_struct_atom.hydrogen_type
_struct_atom.PDB_res_id
_struct_atom.back
_struct_atom.forward
_struct_atom.extra
_struct_atom.psi_id
_struct_atom.distance
_struct_atom.theta
_struct_atom.psi
_struct_atom.radius
_struct_atom.ion_radius
1 NT3 D 4 -1 2 0 . -1.00 -1.00 0.00 1.60 1.32
2 CH2 N 4 1 3 0 . 1.48 -1.00 0.00 1.92 0.00
3 C N 4 2 5 0 . 1.57 112.50 0.00 1.75 0.00
4 O A 4 3 0 0 cO5T 1.27 120.80 -173.09 1.52 1.28
5 NH1 D 5 3 6 0 vl 1.32 111.64 170.14 1.60 1.32
6 CH1 N 5 5 10 0 vll 1.49 128.66 -179.66 1.95 0.00
7 CH1 N 5 6 9 0 Co1C 1.57 110.50 -122.63 1.95 0.00
8 OH1 B 5 7 0 0 Co1C 1.50 109.60 117.40 1.52 1.28
9 CH3 N 5 7 0 0 vv 1.51 110.50 -174.96 1.94 0.00
10 C N 5 6 12 0 vll 1.53 111.20 -102.91 1.75 0.00
11 O A 5 10 0 0 cO5T 1.27 120.80 -175.66 1.52 1.28
12 NH1 D 6 10 13 0 vl 1.32 118.70 143.02 1.60 1.32
13 CH1 N 6 12 17 0 vll 1.50 120.28 179.63 1.95 0.00
14 CH1 N 6 13 16 0 Co1C 1.54 111.50 -125.07 1.95 0.00
15 CH3 N 6 14 0 0 Co1C 1.52 110.50 -123.26 1.94 0.00
16 CH3 N 6 14 0 0 vv 1.56 110.50 178.14 1.94 0.00
17 C N 6 13 19 0 vll 1.56 111.20 -135.03 1.75 0.00
18 O A 6 17 0 0 cO5T 1.27 120.80 -179.08 1.52 1.28
19 NH1 D 7 17 20 0 vl 1.29 114.76 137.41 1.60 1.32
20 CH1 N 7 19 23 0 vll 1.49 115.11 177.44 1.95 0.00
21 CH2 N 7 20 22 0 Co1C 1.50 110.50 -115.85 1.92 0.00
22 S A 7 21 0 0 vv 1.82 114.40 -76.34 1.88 0.40
23 C N 7 20 25 0 vll 1.53 111.20 -67.93 1.75 0.00
24 O A 7 23 0 0 cO5T 1.23 120.80 -179.12 1.52 1.28
25 NH1 D 8 23 26 0 vl 1.30 117.54 147.00 1.60 1.32
26 CH1 N 8 25 31 0 vll 1.46 125.95 174.67 1.95 0.00
27 CH2 N 8 26 28 0 Co1C 1.55 110.50 -122.56 1.92 0.00
28 CH1 N 8 27 30 0 vv 1.53 116.30 0.00 1.95 0.00
29 CH3 N 8 28 0 0 Co1C 1.52 110.70 0.00 1.94 0.00
30 CH3 N 8 28 0 0 vv 1.52 110.70 0.00 1.94 0.00
31 C N 8 26 -1 0 vll 1.57 111.20 -53.91 1.75 0.00
32 O A 8 31 0 0 vf1 1.27 120.80 136.78 1.52 1.28
33 NH1 D 95 -1 34 0 . -1.00 -1.00 0.00 1.60 1.32
34 CH1 N 95 33 38 0 . 1.46 -1.00 0.00 1.95 0.00
35 CH1 N 95 34 37 0 Co1C 1.62 110.50 -127.20 1.95 0.00
36 OH1 B 95 35 0 0 Co1C 1.46 109.60 124.19 1.52 1.28
37 CH3 N 95 35 0 0 vv 1.52 110.50 -45.78 1.94 0.00
38 C N 95 34 40 0 . 1.53 111.20 0.00 1.75 0.00
39 O A 95 38 0 0 cO5T 1.25 120.80 -179.13 1.52 1.28
40 NH1 D 96 38 41 0 vl 1.33 123.74 -3.31 1.60 1.32
41 CH1 N 96 40 44 0 vll 1.44 124.17 -177.27 1.95 0.00
42 CH2 N 96 41 43 0 Co1C 1.57 110.50 -127.44 1.92 0.00
43 S A 96 42 0 0 vv 1.83 114.40 63.21 1.88 0.40
44 C N 96 41 46 0 vll 1.54 111.20 -145.39 1.75 0.00
45 OC A 96 44 0 0 Co1P 1.22 121.00 180.00 1.52 1.28
46 OC A 96 44 -1 0 vv 1.26 121.00 179.67 1.52 1.28
47 S A 97 -1 51 0 . -1.00 -1.00 0.00 1.88 0.40
48 OS A 97 47 0 0 CO7S 1.46 120.19 132.82 1.52 1.28
49 OS A 97 47 0 0 CO8S 1.47 105.54 -102.60 1.52 1.28
50 OS A 97 47 0 0 . 1.51 101.94 0.00 1.52 1.28
51 OS A 97 47 -1 0 . 1.53 101.94 0.00 1.52 1.28
52 OH2 B 215 -1 0 0 . -1.00 -1.00 0.00 1.52 1.28
53 OH2 B 216 -1 0 0 . -1.00 -1.00 0.00 1.52 1.28
54 OH2 B 217 -1 0 0 . -1.00 -1.00 0.00 1.52 1.28
55 OH2 B 218 -1 0 0 . -1.00 -1.00 0.00 1.52 1.28
56 OH2 B 219 -1 0 0 . -1.00 -1.00 0.00 1.52 1.28
57 OH2 B 220 -1 0 0 . -1.00 -1.00 0.00 1.52 1.28
58 OH2 B 221 -1 0 0 . -1.00 -1.00 0.00 1.52 1.28
59 OH2 B 222 -1 0 0 . -1.00 -1.00 0.00 1.52 1.28
Restrain file: new.rst
global_
_entry.id 2SAR
_struct.keywords 'HYDROLASE (ENDORIBONUCLEASE)'
_autid.creation_date 13-DEC-90
_struct.title 'RIBONUCLEASE SA (E.C.3.1.4.8) COMPLEX'
_lib.name mon_lib
_lib.version 3.0
_lib.update 31/05/00
# ------------------------------------------------
data_restraints
#
loop_
#
_restr.record
_restr.number
_restr.label
_restr.period
_restr.atom_id_1
_restr.atom_id_2
_restr.atom_id_3
_restr.atom_id_4
_restr.value
_restr.dev
_restr.val_obs
_restr.dist
_restr.dist_dev
_restr.econst
# data_restr_GLY______0004-_AA
BOND 1 coval . 1 2 . . 1.491 0.021 1.482
. . 422.000 # N CA
BOND 2 coval . 2 3 . . 1.516 0.018 1.567
. . 405.000 # CA C
BOND 3 coval . 3 4 . . 1.231 0.020 1.265
. . 580.000 # C O
ANGL 1 . . 1 2 3 . 112.500 2.900 102.042
2.500 0.042 70.000 # N CA C
ANGL 2 . . 2 3 4 . 120.800 2.100 118.329
2.393 0.025 85.000 # CA C O
# link_'TRANS '_GLY______0004-_AA-THR______0005-_AA
BOND 4 coval . 3 5 . . 1.329 0.014 1.316
. . 471.000 # C N
ANGL 3 . . 4 3 5 . 123.000 1.600 129.584
2.250 0.017 65.000 # O C N
ANGL 4 . . 2 3 5 . 116.200 2.000 111.644
2.417 0.026 20.000 # CA C N
ANGL 5 . . 3 5 6 . 121.700 1.800 128.663
2.435 0.021 80.000 # C N CA
TORS 1 psi 2 1 2 3 5 160.000 30.000 170.141
3.645 0.076 0.000 # N CA C N
TORS 2 omega 1 2 3 5 6 180.000 10.000 -179.661
3.796 0.007 10.000 # CA C N CA
TORS 3 phi 3 3 5 6 10 60.000 20.000 -102.910
3.004 0.158 0.000 # C N CA C
PLAN 1 plane1 . 2 . . . 0.020 . -0.010 . . . # CA
PLAN 1 plane1 . 3 . . . 0.020 . 0.039 . . . # C
PLAN 1 plane1 . 4 . . . 0.020 . -0.015 . . . # O
PLAN 1 plane1 . 5 . . . 0.020 . -0.014 . . . # N
# data_restr_THR______0005-_AA
BOND 5 coval . 5 6 . . 1.458 0.019 1.488
. . 422.000 # N CA
BOND 6 coval . 6 7 . . 1.540 0.027 1.565
. . 200.000 # CA CB
BOND 7 coval . 7 8 . . 1.433 0.016 1.501
. . 320.000 # CB OG1
BOND 8 coval . 7 9 . . 1.521 0.033 1.509
. . 200.000 # CB CG2
BOND 9 coval . 6 10 . . 1.525 0.021 1.528
. . 405.000 # CA C
BOND 10 coval . 10 11 . . 1.231 0.020 1.269
. . 580.000 # C O
ANGL 6 . . 7 6 10 . 110.100 1.900 111.073
2.512 0.029 70.000 # CB CA C
ANGL 7 . . 5 6 7 . 110.500 1.700 114.117
2.464 0.025 65.000 # N CA CB
ANGL 8 . . 8 7 9 . 103.300 2.000 105.694
2.317 0.032 50.000 # OG1 CB CG2
ANGL 9 . . 6 7 8 . 109.600 1.500 100.973
2.430 0.022 50.000 # CA CB OG1
ANGL 10 . . 6 7 9 . 110.500 1.700 123.666
2.515 0.026 45.000 # CA CB CG2
ANGL 11 . . 5 6 10 . 111.200 2.800 106.095
2.462 0.041 70.000 # N CA C
ANGL 12 . . 6 10 11 . 120.800 1.700 117.691
2.401 0.020 85.000 # CA C O
TORS 4 chi1 3 5 6 7 9 180.000 15.000 -174.956
3.803 0.017 2.000 # N CA CB CG2
CHIR 1 negativ . 6 5 7 10 2.520 0.020 -2.627
. . 122.628 # CA N CB C
CHIR 2 positiv . 7 6 8 9 2.722 0.020 2.570
. . -117.400 # CB CA OG1 CG2
# link_'TRANS '_THR______0005-_AA-VAL______0006-_AA
BOND 11 coval . 10 12 . . 1.329 0.014 1.318
. . 471.000 # C N
ANGL 13 . . 11 10 12 . 123.000 1.600 123.456
2.250 0.017 65.000 # O C N
ANGL 14 . . 6 10 12 . 116.200 2.000 118.700
2.425 0.026 20.000 # CA C N
ANGL 15 . . 10 12 13 . 121.700 1.800 120.276
2.435 0.021 80.000 # C N CA
TORS 5 psi 2 5 6 10 12 160.000 30.000 143.023
3.644 0.077 0.000 # N CA C N
TORS 6 omega 1 6 10 12 13 180.000 10.000 179.631
3.804 0.007 10.000 # CA C N CA
TORS 7 phi 3 10 12 13 17 60.000 20.000 -135.031
3.004 0.158 0.000 # C N CA C
PLAN 2 plane1 . 6 . . . 0.020 . -0.007 . . . # CA
PLAN 2 plane1 . 10 . . . 0.020 . 0.023 . . . # C
PLAN 2 plane1 . 11 . . . 0.020 . -0.008 . . . # O
PLAN 2 plane1 . 12 . . . 0.020 . -0.008 . . . # N
# data_restr_VAL______0006-_AA
BOND 12 coval . 12 13 . . 1.458 0.019 1.495
. . 422.000 # N CA
BOND 13 coval . 13 14 . . 1.540 0.027 1.540
. . 200.000 # CA CB
BOND 14 coval . 14 15 . . 1.521 0.033 1.524
. . 200.000 # CB CG1
BOND 15 coval . 14 16 . . 1.521 0.033 1.560
. . 200.000 # CB CG2
BOND 16 coval . 13 17 . . 1.525 0.021 1.565
. . 405.000 # CA C
BOND 17 coval . 17 18 . . 1.231 0.020 1.267
. . 580.000 # C O
ANGL 16 . . 14 13 17 . 109.100 2.200 114.513
2.497 0.034 70.000 # CB CA C
ANGL 17 . . 12 13 14 . 111.500 1.700 115.404
2.479 0.025 65.000 # N CA CB
ANGL 18 . . 15 14 16 . 110.800 2.200 109.396
2.504 0.033 45.000 # CG1 CB CG2
ANGL 19 . . 13 14 15 . 110.500 1.700 113.343
2.515 0.026 45.000 # CA CB CG1
ANGL 20 . . 13 14 16 . 110.500 1.700 110.588
2.515 0.026 45.000 # CA CB CG2
ANGL 21 . . 12 13 17 . 111.200 2.800 102.387
2.462 0.041 70.000 # N CA C
ANGL 22 . . 13 17 18 . 120.800 1.700 118.069
2.401 0.020 85.000 # CA C O
TORS 8 chi1 3 12 13 14 16 180.000 15.000 178.136
3.812 0.017 2.000 # N CA CB CG2
CHIR 3 negativ . 13 12 14 17 2.519 0.020 -2.601
. . 125.069 # CA N CB C
CHIR 4 negativ . 14 13 15 16 2.622 0.020 -2.631
. . 123.263 # CB CA CG1 CG2
# link_'TRANS '_VAL______0006-_AA-CYS______0007-_AA
BOND 18 coval . 17 19 . . 1.329 0.014 1.291
. . 471.000 # C N
ANGL 23 . . 18 17 19 . 123.000 1.600 127.165
2.250 0.017 65.000 # O C N
ANGL 24 . . 13 17 19 . 116.200 2.000 114.758
2.425 0.026 20.000 # CA C N
ANGL 25 . . 17 19 20 . 121.700 1.800 115.110
2.435 0.021 80.000 # C N CA
TORS 9 psi 2 12 13 17 19 160.000 30.000 137.405
3.644 0.077 0.000 # N CA C N
TORS 10 omega 1 13 17 19 20 180.000 10.000 177.436
3.804 0.007 10.000 # CA C N CA
TORS 11 phi 3 17 19 20 23 60.000 20.000 -67.927
3.004 0.158 0.000 # C N CA C
PLAN 3 plane1 . 13 . . . 0.020 . -0.001 . . . # CA
PLAN 3 plane1 . 17 . . . 0.020 . 0.005 . . . # C
PLAN 3 plane1 . 18 . . . 0.020 . -0.002 . . . # O
PLAN 3 plane1 . 19 . . . 0.020 . -0.002 . . . # N
# data_restr_CYS______0007-_AA
BOND 19 coval . 19 20 . . 1.458 0.019 1.488
. . 422.000 # N CA
BOND 20 coval . 20 21 . . 1.530 0.020 1.500
. . 200.000 # CA CB
BOND 21 coval . 21 22 . . 1.808 0.023 1.817
. . 450.000 # CB SG
BOND 22 coval . 20 23 . . 1.525 0.021 1.533
. . 405.000 # CA C
BOND 23 coval . 23 24 . . 1.231 0.020 1.228
. . 580.000 # C O
ANGL 26 . . 21 20 23 . 110.100 1.900 108.208
2.504 0.029 70.000 # CB CA C
ANGL 27 . . 19 20 21 . 110.500 1.700 106.605
2.455 0.025 65.000 # N CA CB
ANGL 28 . . 20 21 22 . 114.400 2.300 109.381
2.810 0.036 50.000 # CA CB SG
ANGL 29 . . 19 20 23 . 111.200 2.800 107.509
2.462 0.041 70.000 # N CA C
ANGL 30 . . 20 23 24 . 120.800 1.700 118.173
2.401 0.020 85.000 # CA C O
TORS 12 chi1 3 19 20 21 22 180.000 15.000 -76.342
4.104 0.019 2.000 # N CA CB SG
CHIR 5 negativ . 20 19 21 23 2.503 0.020 -2.814
. . 115.848 # CA N CB C
# link_'TRANS '_CYS______0007-_AA-LEU______0008-_AA
BOND 24 coval . 23 25 . . 1.329 0.014 1.301
. . 471.000 # C N
ANGL 31 . . 24 23 25 . 123.000 1.600 124.285
2.250 0.017 65.000 # O C N
ANGL 32 . . 20 23 25 . 116.200 2.000 117.536
2.425 0.026 20.000 # CA C N
ANGL 33 . . 23 25 26 . 121.700 1.800 125.954
2.435 0.021 80.000 # C N CA
TORS 13 psi 2 19 20 23 25 160.000 30.000 146.996
3.644 0.077 0.000 # N CA C N
TORS 14 omega 1 20 23 25 26 180.000 10.000 174.674
3.804 0.007 10.000 # CA C N CA
TORS 15 phi 3 23 25 26 31 60.000 20.000 -53.906
3.004 0.158 0.000 # C N CA C
PLAN 4 plane1 . 20 . . . 0.020 . -0.002 . . . # CA
PLAN 4 plane1 . 23 . . . 0.020 . 0.005 . . . # C
PLAN 4 plane1 . 24 . . . 0.020 . -0.002 . . . # O
PLAN 4 plane1 . 25 . . . 0.020 . -0.001 . . . # N
# data_restr_LEU______0008-_AA
BOND 25 coval . 25 26 . . 1.458 0.019 1.457
. . 422.000 # N CA
BOND 26 coval . 26 27 . . 1.530 0.020 1.554
. . 200.000 # CA CB
BOND 27 coval . 26 31 . . 1.525 0.021 1.570
. . 405.000 # CA C
BOND 28 coval . 31 32 . . 1.231 0.020 1.267
. . 580.000 # C O
ANGL 34 . . 27 26 31 . 110.100 1.900 111.572
2.504 0.029 70.000 # CB CA C
ANGL 35 . . 25 26 27 . 110.500 1.700 108.835
2.455 0.025 65.000 # N CA CB
ANGL 36 . . 25 26 31 . 111.200 2.800 110.067
2.462 0.041 70.000 # N CA C
ANGL 37 . . 26 31 32 . 120.800 1.700 126.268
2.401 0.020 85.000 # CA C O
CHIR 6 negativ . 26 25 27 31 2.503 0.020 -2.663
. . 122.560 # CA N CB C
# data_restr_THR______0095-_AA
BOND 29 coval . 33 34 . . 1.458 0.019 1.463
. . 422.000 # N CA
BOND 30 coval . 34 35 . . 1.540 0.027 1.624
. . 200.000 # CA CB
BOND 31 coval . 35 36 . . 1.433 0.016 1.458
. . 320.000 # CB OG1
BOND 32 coval . 35 37 . . 1.521 0.033 1.524
. . 200.000 # CB CG2
BOND 33 coval . 34 38 . . 1.525 0.021 1.525
. . 405.000 # CA C
BOND 34 coval . 38 39 . . 1.231 0.020 1.254
. . 580.000 # C O
ANGL 38 . . 35 34 38 . 110.100 1.900 114.918
2.512 0.029 70.000 # CB CA C
ANGL 39 . . 33 34 35 . 110.500 1.700 110.258
2.464 0.025 65.000 # N CA CB
ANGL 40 . . 36 35 37 . 103.300 2.000 113.469
2.317 0.032 50.000 # OG1 CB CG2
ANGL 41 . . 34 35 36 . 109.600 1.500 104.535
2.430 0.022 50.000 # CA CB OG1
ANGL 42 . . 34 35 37 . 110.500 1.700 113.569
2.515 0.026 45.000 # CA CB CG2
ANGL 43 . . 33 34 38 . 111.200 2.800 109.247
2.462 0.041 70.000 # N CA C
ANGL 44 . . 34 38 39 . 120.800 1.700 119.388
2.401 0.020 85.000 # CA C O
TORS 16 chi1 3 33 34 35 37 180.000 15.000 -45.778
3.803 0.017 2.000 # N CA CB CG2
CHIR 7 negativ . 34 33 35 38 2.520 0.020 -2.556
. . 127.196 # CA N CB C
CHIR 8 positiv . 35 34 36 37 2.722 0.020 2.649
. . -124.193 # CB CA OG1 CG2
# link_'TRANS '_THR______0095-_AA-CYS______0096-_AA
BOND 35 coval . 38 40 . . 1.329 0.014 1.325
. . 471.000 # C N
ANGL 45 . . 39 38 40 . 123.000 1.600 116.866
2.250 0.017 65.000 # O C N
ANGL 46 . . 34 38 40 . 116.200 2.000 123.741
2.425 0.026 20.000 # CA C N
ANGL 47 . . 38 40 41 . 121.700 1.800 124.167
2.435 0.021 80.000 # C N CA
TORS 17 psi 2 33 34 38 40 160.000 30.000 -3.309
3.644 0.077 0.000 # N CA C N
TORS 18 omega 1 34 38 40 41 180.000 10.000 -177.268
3.804 0.007 10.000 # CA C N CA
TORS 19 phi 3 38 40 41 44 60.000 20.000 -145.385
3.004 0.158 0.000 # C N CA C
PLAN 5 plane1 . 34 . . . 0.020 . -0.002 . . . # CA
PLAN 5 plane1 . 38 . . . 0.020 . 0.004 . . . # C
PLAN 5 plane1 . 39 . . . 0.020 . -0.001 . . . # O
PLAN 5 plane1 . 40 . . . 0.020 . -0.001 . . . # N
# data_restr_CYS______0096-_AA
BOND 36 coval . 40 41 . . 1.458 0.019 1.440
. . 422.000 # N CA
BOND 37 coval . 41 42 . . 1.530 0.020 1.569
. . 200.000 # CA CB
BOND 38 coval . 42 43 . . 1.808 0.023 1.826
. . 450.000 # CB SG
BOND 39 coval . 41 44 . . 1.525 0.021 1.537
. . 405.000 # CA C
BOND 40 coval . 44 45 . . 1.231 0.020 1.220
. . 580.000 # C O
BOND 41 coval . 44 46 . . 1.231 0.020 1.258
. . 580.000 # C OXT
ANGL 48 . . 42 41 44 . 110.100 1.900 113.928
2.504 0.029 70.000 # CB CA C
ANGL 49 . . 40 41 42 . 110.500 1.700 106.960
2.455 0.025 65.000 # N CA CB
ANGL 50 . . 41 42 43 . 114.400 2.300 114.904
2.810 0.036 50.000 # CA CB SG
ANGL 51 . . 40 41 44 . 111.200 2.800 114.787
2.462 0.041 70.000 # N CA C
ANGL 52 . . 41 44 45 . 121.000 3.000 117.189
2.403 0.035 85.000 # CA C O
ANGL 53 . . 41 44 46 . 121.000 3.000 118.454
2.403 0.035 85.000 # CA C OXT
TORS 20 chi1 3 40 41 42 43 180.000 15.000 63.207
4.104 0.019 2.000 # N CA CB SG
TORS 21 psi 2 40 41 44 46 160.000 30.000 179.673
3.588 0.069 0.000 # N CA C OXT
CHIR 9 negativ . 41 40 42 44 2.503 0.020 -2.395
. . 127.437 # CA N CB C
PLAN 6 oxt . 44 . . . 0.020 . 0.015 . . . # C
PLAN 6 oxt . 41 . . . 0.020 . -0.004 . . . # CA
PLAN 6 oxt . 45 . . . 0.020 . -0.005 . . . # O
PLAN 6 oxt . 46 . . . 0.020 . -0.005 . . . # OXT
# data_restr_SO4______0097-_Aa
BOND 42 coval . 47 48 . . 1.460 0.020 1.456
. . 525.000 # S O1
BOND 43 coval . 47 49 . . 1.460 0.020 1.474
. . 525.000 # S O2
BOND 44 coval . 47 50 . . 1.460 0.020 1.512
. . 525.000 # S O3
BOND 45 coval . 47 51 . . 1.460 0.020 1.531
. . 525.000 # S O4
ANGL 54 . . 49 47 50 . 109.470 3.000 98.634
2.384 0.044 140.000 # O2 S O3
ANGL 55 . . 50 47 51 . 109.470 3.000 101.943
2.384 0.044 140.000 # O3 S O4
ANGL 56 . . 49 47 51 . 109.470 3.000 105.544
2.384 0.044 140.000 # O2 S O4
ANGL 57 . . 48 47 49 . 109.470 3.000 109.750
2.384 0.044 140.000 # O1 S O2
ANGL 58 . . 48 47 50 . 109.470 3.000 118.079
2.384 0.044 140.000 # O1 S O3
ANGL 59 . . 48 47 51 . 109.470 3.000 120.191
2.384 0.044 140.000 # O1 S O4
# link_'SS '_CYS______0007-_AA-CYS______0096-_AA
BOND 46 disulf . 22 43 . . 2.031 0.020 1.960
. . 500.000 # SG SG
ANGL 60 . . 21 22 43 . 110.000 3.000 107.729
3.147 0.057 50.000 # CB SG SG
ANGL 61 . . 22 43 42 . 110.000 3.000 110.080
3.147 0.057 50.000 # SG SG CB
TORS 22 ss 2 21 22 43 42 90.000 10.000 -90.361
4.056 0.124 3.500 # CB SG SG CB