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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2i4p
TRANSCRIPTION HEADER
CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PPARGAMMA AND THE PARTIAL AGONIST LT127 (UREIDOFIBRATE DERIVATIVE). STRUCTURE OBTAINED FROM CRYSTALS OF THE APO-FORM SOAKED FOR 30 DAYS. TITLE
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA; 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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DRH A 999
226A PHE
228A LEU
281A ILE
282A PHE
284A GLY
285A CYS
286A GLN
288A ARG
289A SER
292A ALA
295A GLU
296A ILE
323A HIS
325A ILE
326A ILE
327A TYR
329A MET
330A LEU
333A LEU
339A VAL
340A LEU
341A ILE
342A SER
348A MET
353A LEU
363A PHE
364A MET
367A LYS
449A HIS
453A LEU
469A LEU
473A TYR
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
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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
2zk0 Details
other holo-structures
pdb ID Ligand Unique ID
3cdp YRGA___1 Details
2zk4 OCRA___1 Details
OCRB___2
3cds GRRA___1 Details
2zno S44B_902 Details
S44A_901
3an3 M7SB___1 Details
2zk2 GSHB___1 PTGA_477 Details
3hod ZZHA___1 Details
2i4z DRHA_999 Details
2zk6 C08B___2 Details
C08A___1
2i4j DRJA_999 Details
2zk1 PTGA___1 Details
PTGB___2
3b3k LRGA___1 Details
2zk3 OCXA___1 Details
OCXB___2
3ho0 DKDA___1 Details
3an4 M7RB___1 Details
3d6d LRGA___1 Details
2zk5 NROB___2 Details
NROA___1
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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DRH NAME: not_found
FORMULA: not_found
SMILES: not_found
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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