university lille north of france LigASite database of binding sites
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LigASite v6.0 (nr25) - non-redundant
LigASite v6.0 (redundant) - redundant
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apo-structureHelp

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

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1bhs
OXIDOREDUCTASE HEADER
HUMAN ESTROGENIC 17BETA-HYDROXYSTEROID DEHYDROGENASE TITLE
17BETA-HYDROXYSTEROID DEHYDROGENASE 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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8 THR
9 GLY
11 SER
12 SER
13 GLY
14 ILE
15 GLY
35 THR
36 LEU
37 ARG
38 ASP
41 THR
44 ARG
64 LEU
65 ASP
66 VAL
67 ARG
90 ASN
91 ALA
92 GLY
93 LEU
94 GLY
95 LEU
96 LEU
113 VAL
140 THR
141 GLY
142 SER
143 VAL
144 GLY
147 MET
149 LEU
150 PRO
152 ASN
155 TYR
156 CYS
159 LYS
185 CYS
186 GLY
187 PRO
188 VAL
190 THR
191 ALA
192 PHE
193 MET
194 GLU
218 TYR
221 HIS
222 SER
225 VAL
226 PHE
258 ARG
259 PHE
262 LEU
279 MET
282 GLU
283 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:

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» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
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
3dhe ANDD_400 21 86 Details
ANDC_400 21 82
1qyw 5SDC_500 21 83 Details
NAPC_361 27 107
5SDD_500 21 88
NAPD_361 27 111
1qyx ASDD_500 21 83 Details
NAPC_361 27 108
ASDC_500 21 83
NAPD_361 27 111
1dht DHTC_400 21 90 Details
DHTD_400 21 84
1jtv TESC_500 21 75 Details
TESD_500 21 81
1equ EQIC_286 NAPC_285 68 256 Details
NAPC_287 48 178
1qyv NAPC_361 48 164 Details
NAPD_361 48 162
1i5r GOLB_401 HYCB_301 55 242 Details
v6.0
October 2008		 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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