university lille north of france LigASite database of binding sites
apo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1uyl
CHAPERONE HEADER
STRUCTURE-ACTIVITY RELATIONSHIPS IN PURINE-BASED INHIBITOR BINDING TO HSP90 ISOFORMS TITLE
HEAT SHOCK PROTEIN HSP 90-ALPHA COMPND
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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22 PHE
48 LEU
51 ASN
52 SER
54 ASP
55 ALA
57 ASP
58 LYS
61 TYR
91 ILE
93 ASP
96 ILE
97 GLY
98 MET
102 ASP
103 LEU
106 ASN
107 LEU
108 GLY
109 THR
110 ILE
111 ALA
132 GLY
135 GLY
136 VAL
137 GLY
138 PHE
139 TYR
150 VAL
154 HIS
162 TRP
170 PHE
184 THR
186 VAL
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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holo-structuresHelp

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
2wi7 2KLA1224 31 133 Details
1uyk PUXA1224 25 112 Details
2vcj 2EQB1224 32 141 Details
2EQD1224 32 143
2vci 2GJB1225 34 141 Details
2GJD1225 34 139
1uyc PU7A1224 25 109 Details
2uwd 2GGB1228 27 129 Details
2GGF1228 27 125
2wi1 ZZ2C1225 13 70 Details
2wi4 ZZ4A1224 23 105 Details
1uy6 PU3A1224 27 117 Details
1uy8 PU5A1224 23 110 Details
2wi6 ZZ6A1224 23 100 Details
1uyd PU8A1224 28 115 Details
1uyh PU0A1224 26 106 Details
1uy9 PU6A1224 24 112 Details
1uyg PU2A1224 22 103 Details
2wi5 ZZ5B1225 25 118 Details
ZZ5A1225 25 121
1uyf PU1A1224 30 120 Details
1uye PU9A1224 29 129 Details
1uy7 PU4A1224 23 105 Details
2cdd CT5B1224 26 114 Details
CT5D1224 26 111
v9.7
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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