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LigASite database of binding sites |
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PDB ID and HEADER , TITLE and
COMPND records of the PDB file. | (click anywhere in this window to remove it) |
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1ade |
LIGASE (SYNTHETASE) |
HEADER |
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STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE PH 7 AT 25 DEGREES CELSIUS |
TITLE |
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ADENYLOSUCCINATE SYNTHETASE |
COMPND |
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Figure highlighting the binding site residues. Figures were drawn with
Molscript (7) and rendered with
Raster3D (8). PISA coordinates
(3) are used when available
(all entries except NMR). | (click anywhere in this window to remove it) |
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List of binding site residues detected in this protein. Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand. Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type. Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein. | (click anywhere in this window to remove it) |
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11 | |
TRP |
12 | |
GLY |
13 | |
ASP |
14 | |
GLU |
15 | |
GLY |
16 | |
LYS |
17 | |
GLY |
18 | |
LYS |
19 | |
ILE |
38 | |
ASN |
39 | |
ALA |
40 | |
GLY |
41 | |
HIS |
42 | |
THR |
44 | |
VAL |
| 49 | |
LYS |
114 | |
ASP |
126 | |
ILE |
127 | |
GLY |
128 | |
THR |
129 | |
THR |
130 | |
GLY |
131 | |
ARG |
133 | |
ILE |
134 | |
GLY |
143 | |
ARG |
223 | |
ALA |
224 | |
GLN |
225 | |
GLY |
228 | |
LEU |
| 237 | |
TYR |
238 | |
VAL |
239 | |
THR |
240 | |
SER |
267 | |
LYS |
272 | |
ARG |
273 | |
VAL |
274 | |
GLY |
275 | |
ALA |
293 | |
GLN |
294 | |
GLY |
295 | |
ASN |
296 | |
GLU |
298 | |
GLY |
299 | |
ALA |
| 300 | |
THR |
301 | |
THR |
303 | |
ARG |
305 | |
ARG |
330 | |
THR |
331 | |
LYS |
333 | |
ASP |
334 | |
VAL |
383 | |
PHE |
414 | |
SER |
416 | |
GLY |
417 | |
PRO |
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PDB |
The Protein Data Bank |
CSA |
Catalytic Site Atlas |
PDBSum |
Overview of the macromolecular structure |
CATH |
Protein Structure Classification |
Scop |
Structural Classification of Proteins |
Pfam |
Protein Families and Domains |
UniProt |
Universal Protein Resource |
LIGPLOT (only on holo-pages) is hosted at the EBI. The LigPlot Jmol links point directly to the Jmol visualisation interface provided on the PDBSum page. Note that due to different software used, the atomic contacts of LigPlot and LigASite do not necessarily correspond. | (click anywhere in this window to remove it) |
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Links to external databases: |
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Several files are provided for download: • The XML file defining the residue-ligand contacts; this file contains data on the apo and all holo-structures. |
• The XML Schema file defining the semantics of the XML file |
• 3D coordinates of the structure used in constructing LigASite (PISA structure file whenever available, PDB file otherwise. |
• 3D coordinates of the combined binding residues in the apo structure |
• 3D coordinates of the binding residues of the holo structure (only on the holo page) |
Coordinate files are in PDB format. | (click anywhere in this window to remove it) |
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Table describing the holo-structures and ligands used to define
the binding sites.
Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand;
a space-separated list of HET -groups that constitute
the ligand (see Methods).
Each HET -group in the ligand is uniquely identified by
a string in which the first four characters are the three-letter
HET ID from the PDB file followed by the chain ID from
the PISA file, and the last four characters are the residue sequence
number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic
contacts. | (click anywhere in this window to remove it) |
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pdb ID |
Ligand Unique ID |
#atoms |
#contacts |
1ksz |
GDPB_432 PGSB_440 _MGB_435 HADB_437 |
64 |
250 |
Details |
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GDPA_432 HADA_437 PGSA_440 _MGA_435 |
64 |
258 |
1gin |
GDPA_432 NO3A_433 IMPA_440 HADA_438 _MGA_435 |
64 |
252 |
Details |
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GDPB_432 IMPB_440 NO3B_433 _MGB_435 HADB_438 |
64 |
256 |
1qf4 |
GDPD___1 PO4D___2 _MGD___3 RPDD___4 |
64 |
239 |
Details |
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GDPC___1 PO4C___2 RPDC___4 _MGC___3 |
64 |
238 |
1son |
AMPB_453 |
23 |
102 |
Details |
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AMPA_453 |
23 |
98 |
1cib |
GDPD_432 IMPD_440 _MGD_434 HDAD_437 NO3D_433 |
64 |
253 |
Details |
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GDPC_432 _MGC_434 NO3C_433 IMPC_440 HDAC_437 |
64 |
256 |
1ch8 |
GPXD_432 IMPD_440 _MGD_434 HDAD_437 NO3D_433 |
67 |
254 |
Details |
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GPXC_432 _MGC_434 NO3C_433 IMPC_440 HDAC_437 |
67 |
256 |
1qf5 |
GDPC___1 PO4C___2 _MGC___3 RPLC___4 |
64 |
243 |
Details |
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GDPD___1 PO4D___2 _MGD___3 RPLD___4 |
64 |
243 |
1soo |
HNPB_453 SO4B_443 _NAB_547 SO4B_442 |
30 |
146 |
Details |
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HNPA_453 SO4A_443 SO4A_442 _NAA_547 |
30 |
142 |
1gim |
GDPA_432 NO3A_433 IMPA_440 HADA_438 _MGA_435 |
64 |
251 |
Details |
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GDPB_432 IMPB_440 NO3B_433 _MGB_435 HADB_438 |
64 |
247 |
1hoo |
GNHC_432 GNPC_432 |
60 |
157 |
Details |
1hop |
GCPA_432 |
32 |
125 |
Details |
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GCPB_433 |
32 |
123 |
1nht |
GDPA_432 HADA_437 SPGA_440 _MGA_435 |
64 |
258 |
Details |
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GDPB_432 _MGB_435 HADB_437 SPGB_440 |
64 |
249 |
2gcq |
DOID_451 GDPD_432 _MGB_435 HADD_437 |
63 |
244 |
Details |
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DOIC_451 HADC_437 GDPC_432 _MGA_435 |
63 |
244 |
1hon |
GNHC_432 |
28 |
114 |
Details |
1juy |
GDPB_432 _PIB_434 _MGB_435 HDAB_438 H5PB_433 |
61 |
239 |
Details |
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GDPA_432 _PIA_434 H5PA_433 HDAA_438 _MGA_435 |
61 |
244 |
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v4.0 May 2008 |
Interdisciplinary Research Institute, Computational Biology, Villeneuve d'Ascq, France University College London, Biomolecular Structure and Modelling Unit, London, UK Hospital for Sick Children and University of Toronto, Structural Biology and Biochemistry Program, Toronto, Canada |
Script execution time: 0.108 seconds |