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

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

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3hvl
TRANSCRIPTION, TRANSFERASE HEADER
TETHERED PXR-LBD/SRC-1P COMPLEXED WITH SR-12813 TITLE
PREGNANE X RECEPTOR, LINKER, STEROID RECEPTOR COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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SRL B 1
206A LEU
209A LEU
211A VAL
240A LEU
243A MET
244A ALA
246A MET
247A SER
251A PHE
281A PHE
284A CYS
285A GLN
288A PHE
299A TRP
306A TYR
308A LEU
323A MET
324A LEU
327A HIS
407A HIS
408A THR
410A ARG
411A LEU
414A ILE
420A PHE
425A MET
429A PHE
SRL D 2
206C LEU
209C LEU
211C VAL
240C LEU
243C MET
244C ALA
246C MET
247C SER
251C PHE
281C PHE
284C CYS
285C GLN
288C PHE
299C TRP
306C TYR
308C LEU
323C MET
324C LEU
327C HIS
407C HIS
408C THR
410C ARG
411C LEU
414C ILE
420C PHE
425C MET
429C PHE
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:

LigPlot (hosted at the EBI):

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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Hide table of related structures
Help

List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
3ctb Details
other holo-structures
pdb ID Ligand Unique ID
none
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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SRL NAME: [2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC ACID DIETHLYL ESTER
FORMULA: C24 H42 O7 P2
SMILES: CCOP(=O)(OCC)C(=Cc1cc(c(O)c(c1)C(C)(C)C)C(C)(C)C)P(=O)(OCC)OCC
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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