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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30 TYR
33 THR
38 ARG
41 ARG
52 GLY
53 LEU
62 ILE
64 ILE
70 LEU
73 HIS
74 ALA
76 TRP
77 SER
80 CYS
81 PHE
84 TRP
86 TRP
112 PHE
113 PRO
120 TYR
124 PHE
126 HIS
138 GLN
140 GLU
142 MET
147 GLN
159 ARG
160 ARG
161 ASP
162 GLY
163 LEU
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
3cnm ACTF_600 HHAG_500 15 90 Details
ACTB_600 HHAD_500 15 92
3juo AJDB_500 17 91 Details
AJDA_500 17 95
3dzl 3OCB_500 3OCB_600 20 104 Details
3OCA_500 3OCA_600 20 97
3b4p 3B4B_500 AZIC_600 19 98 Details
3B4E_500 ACTF_600 20 98
3jup AKDB_500 17 82 Details
AKDA_500 17 87
3jun AJDB_500 AKDB_600 34 161 Details
AJDA_500 AKDA_600 34 163
3jum AODB_500 20 105 Details
AODA_500 20 101
3juq AJDA_500 AKDA_600 34 167 Details
AKDB_600 17 82
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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