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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H26 A 218
110A THR
133A GLU
135A ILE
136A ILE
137A ASP
138A THR
139A GLY
140A LYS
141A THR
142A MET
165A LYS
186A PHE
187A VAL
188A VAL
192A LEU
193A ASP
H26 C 218
110C THR
133C GLU
135C ILE
136C ILE
137C ASP
138C THR
139C GLY
140C LYS
141C THR
142C MET
165C LYS
186C PHE
187C VAL
188C VAL
192C LEU
193C ASP
H26 D 218
103D SER
114D LYS
133D GLU
135D ILE
136D ILE
137D ASP
138D THR
139D GLY
140D LYS
141D THR
142D MET
165D LYS
186D PHE
187D VAL
192D LEU
193D ASP
H26 B 218
114B LYS
133B GLU
135B ILE
136B ILE
137B ASP
138B THR
139B GLY
140B LYS
141B THR
142B MET
165B LYS
186B PHE
187B VAL
192B LEU
193B ASP
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
1z7g Details
other holo-structures
pdb ID Ligand Unique ID
1hmp 5GPD_800 Details
3ggj 25HB_218 Details
3gep 24HC_218 Details
1bzy IMUQ_300 POPT_400 _MGS_900 _MGR_901 Details
IMUB_300 POPE_400 _MGD_900 _MGC_901
IMUG_300 _MGI_900 _MGH_901 POPJ_400
IMUL_300 _MGN_900 POPO_400 _MGM_901
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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H26 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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