university lille north of france LigASite database of binding sites
apo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1ade
LIGASE (SYNTHETASE) HEADER
STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE PH 7 AT 25 DEGREES CELSIUS TITLE
ADENYLOSUCCINATE SYNTHETASE COMPND
Illustration of Binding SiteHelp

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).

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Contacting ResiduesHelp

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.

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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
External LinksHelp

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.

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Links to external databases:

Download FilesHelp

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.

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holo-structuresHelp

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.

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pdb ID Ligand Unique ID #atoms #contacts
1hop GCPA_432 32 125 Details
GCPB_433 32 123
2gcq DOIC_451 HADC_437 GDPC_432 _MGA_435 63 244 Details
DOID_451 GDPD_432 _MGB_435 HADD_437 63 244
1soo HNPB_453 SO4B_443 _NAB_547 SO4B_442 30 146 Details
HNPA_453 SO4A_443 SO4A_442 _NAA_547 30 142
1hoo GNHC_432 GNPC_432 60 157 Details
1son AMPB_453 23 102 Details
AMPA_453 23 98
1nht GDPB_432 _MGB_435 HADB_437 SPGB_440 64 249 Details
GDPA_432 HADA_437 SPGA_440 _MGA_435 64 258
1cib GDPD_432 IMPD_440 _MGD_434 HDAD_437 NO3D_433 64 253 Details
GDPC_432 _MGC_434 NO3C_433 IMPC_440 HDAC_437 64 256
1gim GDPA_432 NO3A_433 IMPA_440 HADA_438 _MGA_435 64 251 Details
GDPB_432 IMPB_440 NO3B_433 _MGB_435 HADB_438 64 247
1gin GDPA_432 NO3A_433 IMPA_440 HADA_438 _MGA_435 64 252 Details
GDPB_432 IMPB_440 NO3B_433 _MGB_435 HADB_438 64 256
1qf5 GDPD___1 PO4D___2 _MGD___3 RPLD___4 64 243 Details
GDPC___1 PO4C___2 _MGC___3 RPLC___4 64 243
1ksz GDPA_432 HADA_437 PGSA_440 _MGA_435 64 258 Details
GDPB_432 PGSB_440 _MGB_435 HADB_437 64 250
1qf4 GDPC___1 PO4C___2 RPDC___4 _MGC___3 64 238 Details
GDPD___1 PO4D___2 _MGD___3 RPDD___4 64 239
1ch8 GPXD_432 IMPD_440 _MGD_434 HDAD_437 NO3D_433 67 254 Details
GPXC_432 _MGC_434 NO3C_433 IMPC_440 HDAC_437 67 256
1juy GDPA_432 _PIA_434 H5PA_433 HDAA_438 _MGA_435 61 244 Details
GDPB_432 _PIB_434 _MGB_435 HDAB_438 H5PB_433 61 239
1hon GNHC_432 28 114 Details
v6.0
October 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
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