university lille north of france LigASite database of binding sites
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LigASite v4.0 (nr25) - non-redundant
LigASite v4.0 (redundant) - redundant
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Browse dataset
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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21 ALA
22 SER
23 GLY
24 LYS
44 GLU
45 ASN
46 GLU
48 LYS
50 ASP
51 ALA
54 PRO
81 HIS
85 TRP
88 GLN
90 PRO
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
373 ASN
374 GLY
408 ASP
409 ALA
410 VAL
411 GLY
412 GLY
417 GLY
421 GLN
423 TYR
424 SER
425 CYS
426 SER
427 ASN
430 ASN
431 GLN
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:

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» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
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
1v6x GCVC_449 XYSC_452 XYSC_450 XYSD_457 XYSD_456 XYSC_451 60 130 Details
GCVE_459 XYSE_462 XYSE_461 XYSE_460 41 70
GCVG_949 XYSG_950 XYSH_957 XYSH_956 XYSG_952 XYSG_951 60 141
1isw XYSG_951 XYSH_956 XYSG_952 XYSH_957 38 130 Details
XYSC_451 XYSC_452 XYSD_457 XYSD_456 38 136
1v6u AHRG_950 XYSH_957 XYSH_956 XYSG_952 XYSG_951 47 154 Details
AHRF_469 XYSF_470 XYSF_471 28 78
XYSC_451 XYSC_452 XYSD_457 XYSD_456 38 125
1v6v AHRC_449 XYSC_452 XYSC_450 XYSD_457 XYSD_456 XYSC_451 56 151 Details
XYSE_461 XYSE_462 XYSE_463 28 71
AHRG_949 XYSG_950 XYSH_957 XYSH_956 XYSG_952 XYSG_951 56 153
AHRF_470 XYSF_472 XYSF_473 XYSF_471 XYSI_473 37 76
1isx XYSG_950 XYSH_957 XYSH_956 XYSG_952 XYSH_958 XYSG_951 56 141 Details
XYSC_450 XYSC_452 XYSD_457 XYSD_456 XYSC_451 47 137
v4.0
May 2008		 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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