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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apo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1fgb
ENTEROTOXIN HEADER
TOXIN TITLE
CHOLERA TOXIN B SUBUNIT PENTAMER 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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11 GLU
12 TYR
13 HIS
14 ASN
31 LEU
32 ALA
33 GLY
34 LYS
35 ARG
51 GLU
56 GLN
57 HIS
58 ILE
61 GLN
88 TRP
90 ASN
91 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:

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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
1rf2 BV4A_106 24 77 Details
BV4A_108 24 75
BV4A_107 24 73
BV4A_104 24 82
1rdp BV3A_104 24 73 Details
BV3A_108 24 76
BV3A_107 24 76
BV3A_106 24 73
1rcv BV1A_105 36 95 Details
BV1A_104 24 75
1pzk J12A_106 21 70 Details
J12A_104 21 71
J12A_108 37 109
J12A_107 21 71
1eei GAAA_504 21 72 Details
GAAA_508 21 73
GAAA_506 21 71
GAAA_507 21 71
1pzj J15A_105 37 106 Details
15BA_104 37 106
J15A_106 37 106
15BA_108 37 107
15BA_107 37 102
1rd9 BV2A_108 37 109 Details
BV2A_105 37 98
BV2A_106 24 72
BV2A_104 24 75
1llr FNGF_104 LNQF_105 45 107 Details
FNGH_104 LNQH_105 45 119
FNGG_104 LNQG_105 45 126
FNGD_104 LNQD_105 45 122
FNGE_104 LNQE_105 45 112
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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