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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60 LEU
64 HIS
67 SER
78 PHE
79 LEU
82 ASN
83 ALA
86 PHE
100 HIS
102 GLY
103 THR
104 ARG
105 PRO
109 GLN
110 TYR
112 THR
113 VAL
116 GLN
117 LEU
131 LEU
134 ILE
135 SER
137 VAL
138 SER
139 HIS
142 LEU
147 GLU
148 GLN
151 HIS
170 LEU
173 ALA
174 LEU
177 MET
178 ASP
182 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
1bjy CTCD_222 _MGE_223 34 147 Details
CTCB_222 33 145
2x9d ITCA1209 33 138 Details
ITCF1209 33 138
1ork ATCC_222 _MGB_223 38 174 Details
ATCF_222 _MGE_223 38 171
2fj1 CTCH_222 _NIJ_223 34 138 Details
CTCC_222 _NIE_223 34 138
2xpt TDCE1209 __KF1210 32 135 Details
TDCK1209 __KL1210 32 137
2xps TDCF_222 _MGE_223 32 133 Details
TDCL_222 _MGK_223 32 142
2xpw OTCE_222 _MGF_223 34 142 Details
OTCL_222 _MGM_223 34 138
2vke TACF_222 _COD_223 33 148 Details
TACL_222 _COJ_223 33 145
2xpv MIYK1209 _MGJ1210 34 146 Details
MIYV1209 _MGU1210 34 137
2x6o 2TCA1209 32 132 Details
2TCD1209 32 134
2xpu TDCD1209 31 130 Details
TDCH1209 31 127
1bj0 CTCD_222 33 143 Details
CTCB_222 33 144
2o7o DXTD_222 _MGE_223 33 142 Details
DXTI_222 _MGJ_223 33 139
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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