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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66 VAL
67 LEU
68 LYS
69 GLY
100 ARG
101 LEU
102 LYS
103 SER
104 TYR
107 ASP
109 SER
110 THR
113 ILE
114 LYS
133 GLU
134 ASP
135 ILE
136 ILE
137 ASP
138 THR
139 GLY
140 LYS
141 THR
142 MET
165 LYS
185 LYS
186 PHE
187 VAL
188 VAL
192 LEU
193 ASP
196 GLU
199 ARG
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
1hmp 5GPD_800 24 90 Details
5GPB_300 24 97
5GPH_800 24 88
5GPF_300 24 99
3ggc H26A_218 19 86 Details
H26D_218 19 78
H26B_218 19 74
H26C_218 19 84
3ggj 25HB_218 20 78 Details
25HD_218 20 79
25HC_218 20 86
25HA_218 20 94
3gep 24HC_218 21 100 Details
24HA_218 21 95
24HB_218 21 91
24HD_218 21 90
1bzy IMUQ_300 POPT_400 _MGS_900 _MGR_901 35 153 Details
IMUB_300 POPE_400 _MGD_900 _MGC_901 35 156
IMUG_300 _MGI_900 _MGH_901 POPJ_400 35 153
IMUL_300 _MGN_900 POPO_400 _MGM_901 35 145
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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