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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802 LYS
803 VAL
804 MET
805 ALA
806 SER
807 LYS
808 LYS
810 PRO
811 LEU
812 TRP
831 ILE
833 LYS
836 ASP
837 ASP
838 LEU
840 GLN
841 ASP
845 LEU
867 TYR
869 CYS
879 ILE
880 GLU
881 ILE
882 VAL
883 LYS
884 ASP
885 ALA
886 THR
887 THR
889 ALA
890 LYS
893 GLN
948 HIS
950 ASP
951 ASN
953 MET
961 PHE
963 ILE
964 ASP
965 PHE
966 GLY
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
2a4z BYMA_101 19 87 Details
3ml9 ML9A9999 31 129 Details
3mjw WYFA___1 28 129 Details
2chz 093A2093 24 101 Details
2chw 039A2093 31 125 Details
3p2b P2BA___1 26 116 Details
2a5u QYTA_101 18 89 Details
3sd5 SD5A___1 29 120 Details
3dpd 41AA2040 18 89 Details
2v4l ABJA2093 20 99 Details
1e8z STUA3001 35 139 Details
3lj3 WYEA1109 30 129 Details
WYED1109 30 126
3ml8 ML8A9999 27 115 Details
3ibe L64A1109 45 175 Details
2chx 090A2093 26 112 Details
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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