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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4prg
RECEPTOR HEADER
0072 PARTIAL AGONIST PPAR GAMMA COCRYSTAL TITLE
PROTEIN (PEROXISOME PROLIFERATOR ACTIVATED 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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072 D 4
226C PHE
228C LEU
255C LEU
256C MET
259C GLU
262C ILE
264C PHE
267C ILE
268C THR
269C PRO
277C VAL
278C ALA
280C ARG
281C ILE
282C PHE
284C GLY
285C CYS
286C GLN
288C ARG
289C SER
292C ALA
295C GLU
326C ILE
327C TYR
329C MET
330C LEU
333C LEU
339C VAL
340C LEU
341C ILE
342C SER
348C MET
353C LEU
356C LEU
360C PHE
363C PHE
364C MET
449C HIS
072 B 1
226A PHE
227A PRO
228A LEU
255A LEU
259A GLU
264A PHE
266A HIS
278A ALA
280A ARG
281A ILE
282A PHE
284A GLY
285A CYS
287A PHE
288A ARG
292A ALA
295A GLU
323A HIS
326A ILE
327A TYR
329A MET
330A LEU
333A LEU
339A VAL
340A LEU
341A ILE
342A SER
348A MET
353A LEU
356A LEU
360A PHE
363A PHE
364A MET
449A HIS
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
1prg 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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072 NAME: (+/-)(2S,5S)-3-(4-(4-CARBOXYPHENYL)BUTYL)-2-HEPTYL-4-OXO-5-THIAZOLIDINE
FORMULA: C37 H46 N2 O4 S1
SMILES: CCCCCCCC1SC(CC(=O)N(Cc2ccccc2)Cc3ccccc3)C(=O)N1CCCCc4ccc(cc4)C(O)=O
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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