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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1xyf
HYDROLASE HEADER
ENDO-1,4-BETA-XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS TITLE
ENDO-1,4-BETA-XYLANASE 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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24 LYS
44 GLU
45 ASN
48 LYS
50 ASP
81 HIS
85 TRP
88 GLN
127 ASN
128 GLU
132 ASP
172 TYR
173 ASN
179 TRP
205 GLN
207 HIS
209 ASN
211 GLY
212 SER
236 GLU
266 TRP
272 ASP
273 SER
274 TRP
275 ARG
325 ASP
326 VAL
327 PRO
328 ASN
329 ALA
338 GLN
340 TYR
341 ASP
342 CYS
343 HIS
344 SER
345 ALA
347 ASN
417 GLY
521 ALA
524 LYS
544 GLU
545 ASN
548 LYS
550 ASP
581 HIS
585 TRP
587 SER
588 GLN
627 ASN
628 GLU
632 ASP
639 ARG
672 TYR
673 ASN
679 TRP
705 GLN
707 HIS
709 ASN
711 GLY
712 SER
736 GLU
766 TRP
772 ASP
773 SER
774 TRP
775 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:

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
1v6u AHRB_950 XYPB_952 XYPB_956 XYPB_951 XYPB_957 47 154 Details
XYPA_451 XYPA_452 XYPA_456 XYPA_457 38 125
1isw XYPB_951 XYPB_952 XYPB_956 XYPB_957 38 130 Details
XYPA_451 XYPA_452 XYPA_456 XYPA_457 38 136
1v6x GCVA_449 XYPA_456 XYPA_452 XYPA_451 XYPA_457 XYPA_450 60 130 Details
GCVB_949 XYPB_952 XYPB_950 XYPB_951 XYPB_956 XYPB_957 60 141
GCVA_459 XYPA_462 XYPA_460 XYPA_461 41 70
1v6v AHRA_449 XYPA_456 XYPA_452 XYPA_451 XYPA_457 XYPA_450 56 150 Details
XYPA_461 XYPA_462 XYPA_463 28 71
AHRB_949 XYPB_952 XYPB_950 XYPB_951 XYPB_956 XYPB_957 56 153
1isx XYPB_950 XYPB_952 XYPB_951 XYPB_958 XYPB_956 XYPB_957 56 141 Details
XYPA_450 XYPA_456 XYPA_452 XYPA_451 XYPA_457 47 137
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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