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[ccp4bb]: Mystery molecule
Dear All,
We have refined a structure at 1.35 A resolution and identified an unusual
ligand bound to the protein. It is clearly defined in the density enabling
us to make a good structural template by driving waters into the density.
Using this template we have searched the Beilstein chemical database and
come up with one very convincing hit. The chemical name is:
(2,7,7-carboxymethyl-3,8-dioxo-1,4,6,9-tetraoxa-5lambda5-phosphaspiro[4.4]no
n-2-yl)-acetic acid - I don't know if there is a trivial name.
The empirical formula is C12,H13,O14,P and the Beilstein registry number is
6455461.
This structure fits the density well and here are the refined coordinates:
ATOM 1422 O1 UNK A 301 24.489 -0.984 19.022 1.00 22.34
O
ATOM 1423 C2 UNK A 301 23.495 -1.864 19.032 1.00 23.72
C
ATOM 1424 C3 UNK A 301 23.474 -2.755 20.240 1.00 23.07
C
ATOM 1425 O4 UNK A 301 24.402 -2.209 21.110 1.00 21.47
O
ATOM 1426 P5 UNK A 301 25.128 -1.034 20.485 1.00 29.61
P
ATOM 1427 O6 UNK A 301 25.314 0.467 20.915 1.00 23.72
O
ATOM 1428 C7 UNK A 301 26.694 0.790 20.920 1.00 24.76
C
ATOM 1429 C8 UNK A 301 27.455 -0.443 20.386 1.00 21.71
C
ATOM 1430 O9 UNK A 301 26.623 -1.443 20.066 1.00 19.40
O
ATOM 1431 O10 UNK A 301 28.678 -0.511 20.284 1.00 19.79
O
ATOM 1432 O11 UNK A 301 22.669 -1.927 18.101 1.00 24.08
O
ATOM 1433 C12 UNK A 301 23.723 -4.165 19.842 1.00 23.86
C
ATOM 1434 C13 UNK A 301 23.596 -5.099 21.023 1.00 27.64
C
ATOM 1435 C14 UNK A 301 22.100 -2.525 20.918 1.00 25.22
C
ATOM 1436 C15 UNK A 301 21.709 -1.168 21.329 1.00 26.15
C
ATOM 1437 O16 UNK A 301 22.045 -0.147 20.750 1.00 22.68
O
ATOM 1438 O17 UNK A 301 22.649 -5.958 21.141 1.00 29.96
O
ATOM 1439 O18 UNK A 301 24.491 -4.970 21.910 1.00 25.74
O
ATOM 1440 C19 UNK A 301 27.227 1.229 22.278 1.00 22.92
C
ATOM 1441 C20 UNK A 301 27.205 0.165 23.320 1.00 21.07
C
ATOM 1442 O21 UNK A 301 27.179 0.523 24.602 1.00 21.16
O
ATOM 1443 O22 UNK A 301 27.178 -1.106 23.119 1.00 21.36
O
ATOM 1444 C23 UNK A 301 26.898 1.829 19.812 1.00 26.81
C
ATOM 1445 C24 UNK A 301 26.308 3.195 19.991 1.00 31.63
C
ATOM 1446 O25 UNK A 301 27.097 4.152 20.360 1.00 34.60
O
ATOM 1447 O26 UNK A 301 25.046 3.394 19.772 1.00 34.94
O
ATOM 1448 O27 UNK A 301 20.967 -1.055 22.351 1.00 26.36
O
A bitmat image is also attached (this can be read into Word and Powerpoint
and probably several other packages).
It doesn't look like any 'natural' ligand and may perhaps be some kind of
chelator. Incidently we used the 'EDTA-free Complete' protease inhibitor
cocktail during protein preparation. However, Roche say this is not an
ingredient.
Has anyone seen this molecule before? If so does it have a trivial name and
where is it likely to have come from?
Thanks in advance,
Dave Lawson
-------------------------------
Dr. David M. Lawson
Biological Chemistry Dept.,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.lawson@bbsrc.ac.uk
unk.bmp
