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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19 ASP
35 VAL
52 ILE
55 LYS
56 SER
57 SER
65 VAL
66 LEU
67 GLY
68 GLY
69 VAL
70 ILE
71 ASP
74 TYR
77 GLU
78 ILE
79 GLY
80 VAL
81 ILE
100 GLN
122 ARG
126 GLY
127 TYR
128 GLY
129 SER
130 THR
219 ASP
235 VAL
252 ILE
254 GLY
255 LYS
256 SER
257 SER
266 LEU
267 GLY
268 GLY
269 VAL
270 ILE
271 ASP
274 TYR
277 GLU
278 ILE
279 GLY
280 VAL
281 ILE
297 LYS
300 GLN
419 ASP
435 VAL
452 ILE
455 LYS
456 SER
457 SER
466 LEU
467 GLY
468 GLY
469 VAL
470 ILE
471 ASP
474 TYR
477 GLU
478 ILE
479 GLY
480 VAL
481 ILE
497 LYS
500 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
1f7q DUTE_801 28 99 Details
DUTC_802 28 102
1f7k UMPD_703 20 89 Details
UMPF_703 20 92
UMPB_703 20 94
1f7r UDPF_138 24 106 Details
UDPD_138 24 106
UDPB_138 24 104
1f7p UDPC_701 24 83 Details
UDPE_702 24 96
1f7n UMPF_337 20 89 Details
UMPD_337 20 88
UMPB_337 20 90
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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