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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1v6x
HYDROLASE HEADER
CRYSTAL STRUCTURE OF XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS E-86 COMPLEXED WITH 3(3)-4-O-METHYL-ALPHA- D-GLUCURONOSYL-XYLOTRIOSE TITLE
ENDO-1,4-BETA-D-XYLANASE 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 A 451
44A GLU
45A ASN
48A LYS
85A TRP
88A GLN
266A TRP
274A TRP
XYP A 450
45A ASN
50A ASP
88A GLN
XYP A 452
48A LYS
81A HIS
85A TRP
127A ASN
128A GLU
205A GLN
207A HIS
236A GLU
266A TRP
274A TRP
XYP A 456
85A TRP
128A GLU
172A TYR
173A ASN
205A GLN
207A HIS
274A TRP
275A ARG
XYP A 457
132A ASP
172A TYR
173A ASN
179A TRP
207A HIS
209A ASN
211A GLY
212A SER
275A ARG
XYP A 461
325A ASP
328A ASN
338A GLN
340A TYR
343A HIS
347A ASN
XYP A 462
327A PRO
328A ASN
338A GLN
340A TYR
417A GLY
XYP A 460
340A TYR
341A ASP
343A HIS
GCV A 459
343A HIS
344A SER
345A ALA
XYP B 951
544B GLU
545B ASN
548B LYS
585B TRP
588B GLN
766B TRP
774B TRP
XYP B 950
545B ASN
550B ASP
588B GLN
XYP B 952
548B LYS
581B HIS
585B TRP
627B ASN
628B GLU
705B GLN
707B HIS
736B GLU
766B TRP
774B TRP
XYP B 956
585B TRP
628B GLU
672B TYR
705B GLN
707B HIS
774B TRP
775B ARG
XYP B 957
632B ASP
672B TYR
673B ASN
679B TRP
707B HIS
709B ASN
711B GLY
712B SER
775B 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).

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apo-structure
pdb ID
1xyf Details
other holo-structures
pdb ID Ligand Unique ID
1v6u AHRB_950 XYPB_952 XYPB_956 XYPB_951 XYPB_957 Details
XYPA_451 XYPA_452 XYPA_456 XYPA_457
1isw XYPB_951 XYPB_952 XYPB_956 XYPB_957 Details
XYPA_451 XYPA_452 XYPA_456 XYPA_457
1v6v AHRA_449 XYPA_456 XYPA_452 XYPA_451 XYPA_457 XYPA_450 Details
XYPA_461 XYPA_462 XYPA_463
AHRB_949 XYPB_952 XYPB_950 XYPB_951 XYPB_956 XYPB_957
1isx XYPB_950 XYPB_952 XYPB_951 XYPB_958 XYPB_956 XYPB_957 Details
XYPA_450 XYPA_456 XYPA_452 XYPA_451 XYPA_457
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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GCV NAME: 4-O-METHYL-ALPHA-D-GLUCURONIC ACID
FORMULA: C7 H12 O7
SMILES: COC1C(O)C(O)C(O)OC1C(O)=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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