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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20 TYR
24 ARG
27 ALA
28 SER
29 ASP
41 LYS
44 ASN
45 ARG
46 TYR
47 ARG
48 ASP
49 VAL
52 PHE
111 ASN
115 GLU
116 LYS
120 LYS
179 TRP
180 PRO
181 ASP
182 PHE
183 GLY
215 CYS
216 SER
217 ALA
218 GLY
219 ILE
220 GLY
221 ARG
254 ARG
258 MET
259 GLY
262 GLN
263 THR
266 GLN
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
1no6 794A_322 25 98 Details
2cm8 F16A1299 15 72 Details
2cnf F32A1299 35 98 Details
1nz7 901A_322 47 155 Details
2veu IZ1A1299 41 114 Details
1onz 968A_322 26 90 Details
3eax LZPA_322 48 103 Details
2cm7 IZDA1299 34 106 Details
1nny 515A_322 53 162 Details
2cng GOLA1302 IZEA1299 42 132 Details
1ony 588A_322 41 130 Details
2vew IZ3A1299 40 107 Details
1pxh SNAA_401 48 136 Details
1q1m 234A_322 30 135 Details
1qxk 429A_322 37 145 Details
1xbo IX1A_322 31 137 Details
2cni IZFA1301 47 149 Details
1nl9 989A_322 39 121 Details
1wax LO1A1300 14 70 Details
2cnh IZBA1300 40 88 Details
2bgd T1DA1298 22 86 Details
2vev IZ2A1300 42 109 Details
3eb1 LZQA_322 29 81 Details
2vey IZ5A1300 41 121 Details
2vex IZ4A1300 40 117 Details
1ph0 418A_322 46 151 Details
1pyn 941A_322 43 143 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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