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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1die
ISOMERASE(INTRAMOLECULAR OXIDOREDUCTSE) HEADER
OBSERVATIONS OF REACTION INTERMEDIATES AND THE MECHANISM OF ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE 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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NOJ D 400
15A TRP
25M PHE
53A HIS
87A MET
89A THR
90A THR
93A PHE
134A VAL
136A TRP
180A GLU
182A LYS
214A ASN
216A GLU
219A HIS
244A ASP
254A ASP
256A ASP
290A HIS
292A ASP
294A LYS
NOJ H 400
15E TRP
25I PHE
53E HIS
87E MET
89E THR
90E THR
93E PHE
134E VAL
136E TRP
180E GLU
182E LYS
214E ASN
216E GLU
219E HIS
244E ASP
254E ASP
256E ASP
290E HIS
292E ASP
294E LYS
MG C 399
180A GLU
216A GLU
244A ASP
292A ASP
MG G 399
180E GLU
216E GLU
244E 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
1xla Details
other holo-structures
pdb ID Ligand Unique ID
1xli GLTH_400 _MNF_398 _MNG_399 Details
GLTL_400 _MNK_399 _MNJ_398
GLTD_400 _MNC_399 _MNB_398
GLTP_400 _MNN_398 _MNO_399
1xlf GCOO_400 _MNP_399 Details
GCOC_400 _MND_399
GCOK_400 _MNL_399
GCOG_400 _MNH_399
1xlj XYLB_400 _MNC_399 Details
1xld XYLJ_400 _MNK_398 _MNL_399 Details
XYLB_400 _MND_399 _MNC_398
XYLN_400 _MNP_399 _MNO_398
XYLF_400 _MNH_399 _MNG_398
1xlc XYLL_400 _MGK_399 Details
XYLI_400 _MGH_399
1xlg XYLJ_400 _ALL_399 _MGK_398 Details
XYLN_400 _MGO_398 _ALP_399
1did DIGD_400 _MNC_399 Details
DIGH_400 _MNG_399
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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NOJ NAME: 1-DEOXYNOJIRIMYCIN
FORMULA: C6 H13 N1 O4
SMILES: OCC1NCC(O)C(O)C1O
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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