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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436 PHE
437 TRP
442 ARG
445 TRP
446 GLU
447 THR
448 THR
449 ILE
467 GLN
469 HIS
470 LYS
471 ARG
472 VAL
473 TRP
475 ALA
476 SER
478 ARG
479 ASP
480 VAL
482 TYR
484 SER
504 ASN
521 ALA
523 ILE
525 VAL
553 TYR
555 ALA
557 VAL
559 PRO
563 ALA
564 PRO
567 VAL
568 LEU
571 VAL
572 ALA
574 ARG
575 GLU
576 TYR
578 LYS
579 PHE
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
2e3n 6CMA_600 28 155 Details
3h3s H15B_600 29 128 Details
H15A_600 29 133
2e3q 18CA_600 40 184 Details
2z9y DDRA___1 28 140 Details
3h3t 16HA_600 30 132 Details
16HB_600 30 141
2e3r 18CA1100 40 198 Details
18CB1200 40 195
2e3o 16CA_600 38 186 Details
3h3q H13B_600 27 115 Details
H13A_600 27 129
2e3p 16CB_700 38 199 Details
16CA_600 38 185
3h3r 14HA_600 28 128 Details
14HB_600 28 127
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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