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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6xim
ISOMERASE(INTRAMOLECULAR OXIDOREDUCTSE) HEADER
PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE- DIRECTED MUTAGENESIS OF METAL BINDING SITES TITLE
D-XYLOSE ISOMERASE 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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XLS D 397
16A TRP
26I PHE
54A HIS
88A MET
90A THR
91A THR
94A PHE
135A VAL
137A TRP
181A GLU
183A LYS
215A ASN
217A GLU
220A HIS
245A ASP
255A ASP
257A ASP
292A ASP
294A LYS
XLS H 397
16E TRP
26M PHE
54E HIS
88E MET
90E THR
91E THR
94E PHE
135E VAL
137E TRP
181E GLU
183E LYS
215E ASN
217E GLU
220E HIS
245E ASP
255E ASP
257E ASP
292E ASP
294E LYS
MG C 395
181A GLU
217A GLU
245A ASP
292A ASP
MG G 395
181E GLU
217E GLU
245E ASP
292E ASP
MG B 396
217A GLU
220A HIS
255A ASP
257A ASP
292A ASP
MG F 396
217E GLU
220E HIS
255E ASP
257E ASP
292E 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
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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
7xim Details
other holo-structures
pdb ID Ligand Unique ID
5xim SORL_397 _MGK_395 Details
SORC_397 _MGB_395
SORF_397 _MGE_395
1xim XYLH_397 _COF_396 _COG_395 Details
XYLD_397 _COC_395 _COB_396
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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XLS NAME: D-XYLOSE (LINEAR FORM)
FORMULA: C5 H10 O5
SMILES: OCC(O)C(O)C(O)C=O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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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