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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10 TYR
12 PHE
14 PRO
51 PHE
95 GLY
96 GLY
97 TRP
98 TYR
99 TYR
101 ASN
103 LEU
142 ASP
144 GLU
145 TYR
184 ALA
186 ALA
187 GLY
188 GLY
190 PHE
191 PHE
193 SER
194 ARG
212 MET
214 TYR
215 ASP
216 LEU
217 ALA
220 TRP
221 GLU
239 PHE
265 LEU
292 TYR
294 ARG
314 GLY
316 ASP
317 PRO
318 TYR
333 ARG
334 ASP
336 ASP
339 ILE
401 MET
403 TRP
404 HIS
407 GLN
461 THR
464 GLN
479 TRP
480 GLY
481 TYR
482 ILE
483 THR
484 SER
489 ASP
490 SER
491 ALA
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
1w1v GOLE1500 GOLK1506 12 74 Details
ALJT1520 GOLJ1517 GOLF1509 GOLR1516 36 158
GOLD1500 GOLZ1507 GOLB1512 18 101
ALJK1513 GOLZ1507 GOLB1512 GOLH1510 GOLX1511 GOLY1508 48 216
1e6r AMIL1502 NAAK1501 NAAJ1500 43 148 Details
AMIF1501 NAAE1500 NAAD1499 43 146
1w1p GIOL1518 GOLI1510 GOLK1514 23 94 Details
GOLH1508 GOLV1512 12 72
1ur8 GDLI2502 NAGH2501 29 106 Details
GDLP2502 SO4L1510 NAGO2501 34 120
1w1y TYPJ1508 TYPQ1506 TYPN1507 57 242 Details
GOLS1504 GOLU1503 12 70
TYPD1508 TYPR1509 TYPI1507 57 229
1w1t GOLC1506 GOLP1500 12 77 Details
CHQB1513 CHQY1512 GOLX1507 40 154
CHQI1513 GOLF1508 CHQM1514 GOLG1509 GOLO1500 52 207
1o6i ARGU1520 GOLZ1510 GOLL1513 GOLJ1499 DPRU1519 GOLN1508 GOLH1515 GOLD1512 54 282 Details
ARGA1517 GOLG1511 DPRA1516 24 118
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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