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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3ej2
HYDROLASE HEADER
CRYSTAL STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM BURKHOLDERIA PSEUDOMALLEI WITH BOUND 5-AMINO-1-(4- CHLOROPHENYL)-1H-PYRAZOLE-4-CARBONITRILE, H32 CRYSTAL FORM TITLE
INORGANIC PYROPHOSPHATASE 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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928 C 176
75C ILE
76D THR
77D PRO
117D MET
118D THR
120D ASN
121C LEU
128C PRO
130C TYR
131C LEU
928 D 176
75D ILE
76C THR
77C PRO
117C MET
118C THR
120C ASN
121D LEU
128D PRO
130D TYR
131D LEU
928 A 176
75A ILE
76E THR
77E PRO
117E MET
118E THR
120E ASN
121A LEU
128A PRO
130A TYR
131A LEU
928 E 176
75E ILE
76A THR
77A PRO
117A MET
118A THR
120E ASN
121E LEU
128E PRO
130E TYR
131E LEU
928 B 176
75B ILE
76F THR
77F PRO
117F MET
118F THR
120B ASN
121B LEU
128B PRO
130B TYR
131B LEU
928 F 176
75F ILE
76B THR
77B PRO
117B MET
118B THR
120B ASN
121F LEU
128F PRO
130F TYR
131F LEU
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
3eiz Details
other holo-structures
pdb ID Ligand Unique ID
3ej0 11XA_176 11XA_177 Details
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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928 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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