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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125 MET
126 PRO
127 ARG
128 ILE
129 SER
131 ALA
132 GLN
135 ASP
137 LEU
138 SER
141 SER
178 PHE
179 GLY
180 VAL
181 GLY
182 VAL
183 ALA
185 LEU
201 THR
202 ASP
203 VAL
204 ARG
209 GLU
210 GLN
230 GLU
233 GLY
234 GLY
235 TYR
236 ALA
237 LYS
239 MET
243 PHE
244 ARG
247 GLN
264 THR
265 ALA
266 LEU
267 ILE
268 PRO
273 PRO
274 VAL
275 LEU
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
1u2g APRB_500 36 146 Details
APRD_600 NDPG_400 84 320
1hzz NAPE_300 48 193 Details
NADB_400 44 195
1u28 NADB_500 44 178 Details
NAPH_400 48 189
NADD_600 27 90
2oo5 NAPJ_400 TXDH_600 92 336 Details
TXDD_500 44 179
1f8g NADB2501 35 141 Details
NADD2503 44 168
2oor NADB_500 44 180 Details
TXPG_400 48 189
NADD_600 36 129
1xlt NADE_400 44 138 Details
NDPI_500 48 195
NADC_400 44 161
1l7e NAIB_701 44 189 Details
1u2d NADB_500 44 178 Details
NADD_600 NDPG_400 92 369
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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