university lille north of france LigASite database of binding sites
apo-structureHelp

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

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1xla
ISOMERASE(INTRAMOLECULAR OXIDOREDUCTSE) HEADER
MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT TITLE
D-XYLOSE ISOMERASE COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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15 TRP
25 PHE
53 HIS
56 ASP
87 MET
89 THR
90 THR
93 PHE
134 VAL
136 TRP
180 GLU
182 LYS
214 ASN
216 GLU
219 HIS
244 ASP
254 ASP
256 ASP
290 HIS
292 ASP
294 LYS
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:

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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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
1xli GLTH_400 _MNF_398 _MNG_399 14 83 Details
GLTL_400 _MNK_399 _MNJ_398 14 81
GLTD_400 _MNC_399 _MNB_398 14 79
GLTP_400 _MNN_398 _MNO_399 14 80
1xlf GCOO_400 _MNP_399 14 73 Details
GCOC_400 _MND_399 14 74
GCOK_400 _MNL_399 14 72
GCOG_400 _MNH_399 14 75
1xlj XYLB_400 _MNC_399 11 73 Details
1xld XYLJ_400 _MNK_398 _MNL_399 12 76 Details
XYLB_400 _MND_399 _MNC_398 12 75
XYLN_400 _MNP_399 _MNO_398 12 73
XYLF_400 _MNH_399 _MNG_398 12 76
1xlc XYLL_400 _MGK_399 11 71 Details
XYLI_400 _MGH_399 11 73
1die NOJD_400 _MGC_399 12 71 Details
NOJH_400 _MGG_399 12 74
1xlg XYLJ_400 _ALL_399 _MGK_398 12 71 Details
XYLN_400 _MGO_398 _ALP_399 12 72
1did DIGD_400 _MNC_399 12 70 Details
DIGH_400 _MNG_399 12 70
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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