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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1od8
HYDROLASE/LECTIN HEADER
XYLANASE XYN10A FROM STREPTOMYCES LIVIDANS IN COMPLEX WITH XYLOBIO-ISOFAGOMINE LACTAM TITLE
ENDO-1,4-BETA-XYLANASE A 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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XYP A1311
44A GLU
45A ASN
48A LYS
85A TRP
88A GLN
266A TRP
274A TRP
XDL A1310
48A LYS
81A HIS
85A TRP
127A ASN
128A GLU
205A GLN
207A HIS
236A GLU
266A TRP
274A TRP
IMD A1309
85A TRP
128A GLU
139A ARG
172A TYR
205A GLN
207A HIS
274A TRP
275A ARG
XDL A1306
132A ASP
133A GLY
173A ASN
179A TRP
211A GLY
XYP A1307
132A ASP
172A TYR
173A ASN
207A HIS
209A ASN
211A GLY
212A SER
275A ARG
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
1e0w Details
other holo-structures
pdb ID Ligand Unique ID
1v0n IMDA1307 XYPA1306 XIFA1305 Details
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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IMD NAME: IMIDAZOLE
FORMULA: C3 H5 N2
SMILES: [nH]1cc[nH+]c1
XDL NAME: XYLOSE-DERIVED ISOFAGOMINE LACTAM
FORMULA: C5 H9 N1 O2
SMILES: OC1CCCNC1=O
XYP NAME: BETA-D-XYLOPYRANOSE
FORMULA: C5 H10 O5
SMILES: OC1COC(O)C(O)C1O
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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