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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1tvq
LIPID BINDING PROTEIN HEADER
CRYSTAL STRUCTURE OF APO CHICKEN LIVER BASIC FATTY ACID BINDING PROTEIN (OR BILE ACID BINDING PROTEIN) TITLE
FATTY ACID-BINDING PROTEIN 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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14 TYR
17 PHE
18 LEU
21 LEU
22 ALA
23 LEU
24 PRO
27 LEU
28 ILE
30 MET
31 ALA
34 ILE
36 PRO
38 VAL
40 ILE
49 VAL
51 SER
53 THR
54 PRO
55 ARG
56 GLN
60 ASN
62 PHE
70 ILE
71 THR
72 THR
73 MET
74 ASP
76 LYS
78 LEU
80 CYS
82 VAL
89 LEU
90 VAL
91 THR
95 LYS
96 PHE
97 SER
98 HIS
100 GLN
109 GLU
111 ILE
113 PHE
118 LEU
120 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
1tw4 CHDB1130 CHDB1131 58 216 Details
CHDA_130 CHDA_131 58 220
2jn3 JN3A_130 JN3A_131 56 270 Details
2k62 ITLA_202 _YBA_201 59 142 Details
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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