university lille north of france LigASite database of binding sites

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

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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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H15 B 600
436B PHE
442B ARG
445B TRP
446B GLU
448B THR
449B ILE
467B GLN
469B HIS
472B VAL
473B TRP
478B ARG
479B ASP
480B VAL
482B TYR
504B ASN
521B ALA
523B ILE
525B VAL
553B TYR
557B VAL
559B PRO
568B LEU
571B VAL
572B ALA
575B GLU
576B TYR
579B PHE
H15 A 600
436A PHE
442A ARG
445A TRP
446A GLU
448A THR
449A ILE
467A GLN
469A HIS
470A LYS
472A VAL
473A TRP
478A ARG
479A ASP
480A VAL
482A TYR
504A ASN
521A ALA
523A ILE
525A VAL
553A TYR
557A VAL
571A VAL
572A ALA
575A GLU
576A TYR
579A 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

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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pdb ID
2e3m Details
other holo-structures
pdb ID Ligand Unique ID
2e3n 6CMA_600 Details
2e3q 18CA_600 Details
2z9y DDRA___1 Details
3h3t 16HA_600 Details
2e3r 18CA1100 Details
2e3o 16CA_600 Details
3h3q H13B_600 Details
2e3p 16CB_700 Details
3h3r 14HA_600 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

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H15 NAME: not_found
FORMULA: not_found
SMILES: not_found
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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