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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237 TYR
241 ASN
245 ILE
316 ARG
318 ASP
329 TYR
330 GLU
332 ASN
335 SER
336 ALA
337 SER
338 CYS
341 GLU
387 ASP
389 ASP
391 GLU
392 GLU
394 TYR
395 HIS
441 THR
442 TRP
443 ALA
446 THR
496 GLY
498 LYS
515 LEU
531 ALA
533 LYS
534 PRO
537 GLY
538 ARG
539 CYS
540 GLY
541 SER
543 ILE
545 LEU
568 GLN
569 GLN
570 LEU
571 TRP
572 CYS
573 LEU
582 GLN
598 ARG
603 LEU
604 VAL
605 ILE
606 LYS
607 LYS
608 GLU
609 SER
610 ASP
611 ILE
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
2io9 ADPG3002 _MGJ7004 GSHH5002 _MGI7003 48 225 Details
ADPB3001 _MGE7002 _MGD7001 GSHC5001 48 233
2io7 ANPF_965 _MGH5004 _MGG5003 33 134 Details
ANPB_964 _MGC5001 _MGD5002 33 142
2ioa ADPB3001 _MGE5002 GGAC6001 _MGD5001 62 290 Details
ADPG3002 _MGI5003 _MGJ5004 GGAH6002 62 275
2io8 ADPF5002 _MGH7004 _MGG7003 29 125 Details
ADPB5001 _MGD7002 _MGC7001 29 121
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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