university lille north of france LigASite database of binding sites
apo-structureHelp

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

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1vpn
VIRAL PROTEIN HEADER
UNASSEMBLED POLYOMAVIRUS VP1 PENTAMER TITLE
POLYOMAVIRUS VP1 PENTAMER COMPND
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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71 GLN
72 TYR
77 ARG
78 GLY
79 ILE
80 ASN
81 LEU
82 ALA
83 THR
85 ASP
87 GLU
89 SER
91 GLY
93 ASN
94 THR
186 LYS
289 ARG
291 THR
293 ASN
296 VAL
298 HIS
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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holo-structuresHelp

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
1vps GALT___2 SIAQ___1 SIAR___4 NAGS___3 66 116 Details
GALE___2 SIAC___4 NAGD___3 SIAB___1 66 121
GALI___2 NAGH___3 SIAF___1 SIAG___4 66 123
GALN___2 SIAK___1 SIAL___4 NAGM___3 66 119
GALS___2 NAGR___3 SIAP___1 SIAQ___4 66 116
GALO___2 NAGN___3 SIAL___1 SIAM___4 66 118
GALY___2 SIAV___1 NAGX___3 SIAW___4 66 124
GALD___2 SIAA___1 NAGC___3 SIAB___4 66 121
GALJ___2 SIAG___1 NAGI___3 SIAH___4 66 123
GALX___2 NAGW___3 SIAU___1 SIAV___4 66 124
v9.7
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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