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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15 MET
17 LYS
18 HIS
19 SER
20 LYS
21 SER
22 PHE
26 PHE
37 VAL
40 ILE
41 TYR
44 CYS
45 ARG
48 ASP
49 ASP
52 ASP
53 VAL
107 LEU
111 VAL
129 TYR
133 VAL
134 ALA
137 VAL
138 GLY
141 LEU
142 THR
145 LEU
157 ALA
160 LEU
161 GLY
164 LEU
165 GLN
168 ASN
169 ILE
171 ARG
172 ASP
175 GLU
176 ASP
183 TYR
233 PHE
241 ILE
244 ALA
248 TYR
251 ILE
265 ARG
266 VAL
267 PHE
273 LYS
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
3nri DH7A_288 30 146 Details
3acx 673A1001 23 105 Details
3acy 702A1001 _MGA1002 33 141 Details
2zy1 830A_808 24 112 Details
2zcr B69A_668 _MGA_669 29 146 Details
2zcq B65A_451 _MGA_453 _MGA_452 27 122 Details
2zcs B70A_640 24 118 Details
3npr PS7A1001 _MGA1002 40 172 Details
3acw 651A1001 21 99 Details
2zcp FPSA_657 FPSA_658 _MGA_661 _MGA_663 _MGA_662 51 193 Details
FPSB_659 _MGB_665 _MGB_666 FPSB_660 _MGB_664 51 199
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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