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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1u26
HYDROLASE HEADER
CRYSTAL STRUCTURE OF SELENOMONAS RUMINANTIUM PHYTASE COMPLEXED WITH PERSULFATED PHYTATE TITLE
MYO-INOSITOL HEXAPHOSPHATE PHOSPHOHYDROLASE 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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IHS B2165
46B ARG
58B ASN
72B LYS
138B TYR
141B ARG
142B ASP
174B LEU
178B LYS
212B ASP
213B HIS
241B CYS
242B GLU
243B ALA
245B VAL
246B GLY
247B ARG
278B PHE
288B LYS
291B ASP
293B TRP
294B LYS
298B TYR
301B LYS
IHS A2166
46A ARG
58A ASN
138A TYR
141A ARG
142A ASP
174A LEU
178A LYS
212A ASP
213A HIS
241A CYS
242A GLU
243A ALA
244A GLY
245A VAL
246A GLY
247A ARG
278A PHE
291A ASP
294A LYS
298A TYR
301A LYS
IHS A2167
149A SER
150B GLN
151A HIS
154B LEU
158A ARG
206B PHE
207B ARG
219B GLU
223B ARG
226B ALA
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
1u24 Details
other holo-structures
pdb ID Ligand Unique ID
1u25 IHSJ2165 Details
IHSB2166
IHSC2167 IHSD2167
IHSF2166
IHSH2165
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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IHS NAME: D-MYO-INOSITOL-HEXASULPHATE
FORMULA: C6 H12 O24 S6
SMILES: OS(=O)(=O)OC1C(OS(O)(=O)=O)C(OS(O)(=O)=O)C(OS(O)(=O)=O)C(OS(O)(=O)=O)C1OS(O)(=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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