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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178 ASN
235 THR
236 VAL
237 SER
240 VAL
257 ASN
283 LEU
285 ARG
302 LYS
303 ASP
304 GLY
307 THR
309 GLU
311 LEU
331 VAL
332 SER
335 GLN
337 LEU
359 GLU
360 SER
363 LYS
365 TRP
366 GLN
369 VAL
370 GLY
391 TRP
392 ASP
395 ASP
400 THR
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
1tyx ABEX___3 ABEY___7 RAMZ___4 MANW___6 MANV___2 GLAU___5 GLAT___1 72 120 Details
ABEF___3 MANE___6 ABEG___7 RAMI___8 MAND___2 GLAB___1 RAMH___4 GLAC___5 83 160
ABEO___3 MANN___6 RAMQ___4 GLAL___5 RAMR___8 GLAK___1 ABEP___7 MANM___2 83 158
1tyw GLAB___5 TYVH___7 GLAJ___1 RAME___8 MANC___2 MANF___6 GLCG___9 TYVD___3 RAMI___4 94 203 Details
GLAL___5 TYVN___3 MANP___6 RAMS___4 TYVR___7 RAMO___8 GLAT___1 GLCQ___9 MANM___2 94 202
GLAD___1 MANZ___6 RAMY___8 GLAV___5 TYVB___7 MANW___2 RAMC___4 TYVX___3 GLCA___9 94 204
1tyu GLAE___5 MANF___2 RAMD___4 MANB___6 TYVC___7 RAMH___8 63 113 Details
GLAA___1 RAMZ___8 TYVU___7 GLAW___5 MANT___6 TYVY___3 RAMV___4 MANX___2 83 170
GLAN___5 RAMM___4 GLAR___1 MANO___2 TYVL___7 RAMQ___8 MANK___6 TYVP___3 83 173
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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