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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226 PHE
227 PRO
228 LEU
249 ILE
255 LEU
258 GLY
259 GLU
262 ILE
263 LYS
264 PHE
265 LYS
266 HIS
267 ILE
268 THR
279 ILE
280 ARG
281 ILE
282 PHE
283 GLN
284 GLY
285 CYS
286 GLN
287 PHE
288 ARG
289 SER
290 VAL
291 GLU
292 ALA
293 VAL
295 GLU
296 ILE
323 HIS
325 ILE
326 ILE
327 TYR
329 MET
330 LEU
333 LEU
339 VAL
340 LEU
341 ILE
342 SER
343 GLU
344 GLY
348 MET
353 LEU
360 PHE
363 PHE
364 MET
367 LYS
449 HIS
450 VAL
453 LEU
456 ILE
463 MET
464 SER
465 LEU
469 LEU
473 TYR
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
3cdp YRGA___1 19 100 Details
2zk4 OCRA___1 23 140 Details
OCRB___2 23 149
3cds GRRA___1 20 95 Details
2zno S44B_902 33 145 Details
S44A_901 33 155
3an3 M7SB___1 42 193 Details
2zk2 GSHB___1 PTGA_477 43 220 Details
3hod ZZHA___1 25 125 Details
2i4z DRHA_999 33 162 Details
2zk6 C08B___2 29 155 Details
C08A___1 29 140
2i4j DRJA_999 33 141 Details
2zk1 PTGA___1 23 136 Details
PTGB___2 23 119
3b3k LRGA___1 24 113 Details
2zk3 OCXA___1 23 140 Details
OCXB___2 23 123
3ho0 DKDA___1 26 135 Details
2i4p DRHA_999 33 175 Details
3an4 M7RB___1 42 179 Details
3d6d LRGA___1 24 120 Details
2zk5 NROB___2 22 110 Details
NROA___1 22 110
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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