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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2gub
ISOMERASE HEADER
CRYSTAL STRUCTURE OF METAL FREE D-XYLOSE ISOMERASE. TITLE
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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16 TRP
26 PHE
54 HIS
88 MET
90 THR
91 THR
94 PHE
135 VAL
137 TRP
181 GLU
183 LYS
215 ASN
217 GLU
219 GLY
220 HIS
245 ASP
247 ASN
255 ASP
257 ASP
285 HIS
287 ASP
289 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
3kbn GLOO_401 _NIM_391 _NIN_393 _NIL_392 15 81 Details
GLOT_401 _NIQ_392 _NIS_393 _NIR_391 15 81
GLOJ_401 _NIG_392 _NIH_391 _NII_393 15 80
GLOE_401 _NIB_392 _NIC_391 _NID_393 15 80
3kco GLOS_401 _NIT_393 _NIQ_392 _NIR_391 26 81 Details
GLON_401 _NIO_393 _NIM_391 _NIL_392 26 81
GLOI_401 _NIG_392 _NIJ_393 _NIH_391 26 80
GLOD_401 _NIE_393 _NIB_392 _NIC_391 26 80
3kcl GLCH_401 _CDG_392 _CDF_391 26 80 Details
GLCP_401 _CDN_391 _CDO_392 26 80
GLCL_401 _CDK_392 _CDJ_391 26 80
GLCD_401 _CDB_391 _CDC_392 26 80
3kbm GLCH_401 _CDG_392 13 73 Details
GLCP_401 _CDO_392 13 70
GLCD_401 _CDC_392 13 73
GLCL_401 _CDK_392 13 70
3cwh XULG_401 _MGI_392 _OHJ_501 _MGH_391 23 75 Details
XULL_401 _MGN_392 _MGM_391 _OHO_501 23 79
XULQ_401 _OHT_501 _MGS_392 _MGR_391 23 79
XULB_401 _MGC_391 _MGD_392 _OHE_501 23 75
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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