university lille north of france LigASite database of binding sites

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

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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
297 PHE
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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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
1cg0 GDPB_432 HDAE_437 IMOC_440 _MGD_435 64 252 Details
GDPG_432 IMOH_440 HDAJ_437 _MGI_435 64 248
2gcq DOIG_451 _MGH_435 GDPF_432 HADE_437 63 244 Details
DOIC_451 HADA_437 GDPB_432 _MGD_435 63 244
1hoo GNHB_432 GNPC_432 60 176 Details
1gim GDPG_432 HADF_438 IMPH_440 _MGI_435 NO3J_433 64 262 Details
GDPB_432 HADA_438 _MGD_435 IMPC_440 NO3E_433 64 264
1qf5 GDPB_434 _MGE_433 RPLC_435 PO4D_432 64 240 Details
GDPG_434 _MGJ_433 PO4I_432 RPLH_435 64 240
1qf4 GDPG_434 _MGJ_433 PO4I_432 RPDH_435 64 238 Details
GDPB_434 RPDC_435 _MGE_433 PO4D_432 64 237
1juy GDPB_432 H5PC_433 _PID_434 HDAF_438 _MGE_435 61 257 Details
GDPH_432 HDAL_438 _PIJ_434 H5PI_433 _MGK_435 61 263
1hon GNHB_432 28 134 Details
1hop GCPD_433 32 128 Details
GCPB_432 32 134
1soo H5PE_453 SO4D_442 _NAF_547 SO4C_443 30 142 Details
H5PL_453 SO4K_442 SO4J_443 _NAM_547 30 146
1nht GDPC_432 PGSB_440 HADA_437 _MGD_435 64 267 Details
GDPG_432 _MGH_435 PGSF_440 HADE_437 64 257
1son AMPB_453 23 98 Details
AMPE_453 23 102
1cib GDPH_432 HDAK_437 _MGJ_434 IMPI_440 NO3L_433 64 253 Details
GDPB_432 HDAE_437 NO3F_433 _MGD_434 IMPC_440 64 256
1gin GDPB_432 IMPD_440 _MGC_435 HADA_438 NO3E_433 64 274 Details
GDPG_432 _MGH_435 IMPI_440 HADF_438 NO3J_433 64 274
1ksz GDPC_432 PGSB_440 HADA_437 _MGD_435 64 278 Details
GDPG_432 _MGH_435 PGSF_440 HADE_437 64 273
1ch8 GPXH_432 IMPI_440 NO3L_433 _MGK_434 HDAJ_437 67 254 Details
GPXB_432 NO3F_433 HDAD_437 IMPC_440 _MGE_434 67 255
IMPI_440 NO3L_433 HDAJ_437 35 145
April 2012
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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