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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2jn3
LIPID BINDING PROTEIN HEADER
NMR STRUCTURE OF CL-BABP COMPLEXED TO CHENODEOXYCHOLIC ACID TITLE
FATTY ACID-BINDING PROTEIN, LIVER 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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JN3 A 130
14A TYR
17A PHE
18A LEU
21A LEU
23A LEU
27A LEU
28A ILE
30A MET
31A ALA
34A ILE
36A PRO
38A VAL
53A THR
55A ARG
56A GLN
72A THR
73A MET
74A ASP
98A HIS
109A GLU
111A ILE
118A LEU
120A ARG
JN3 A 131
17A PHE
21A LEU
38A VAL
40A ILE
49A VAL
51A SER
60A ASN
62A PHE
70A ILE
71A THR
72A THR
74A ASP
76A LYS
78A LEU
80A CYS
82A VAL
89A LEU
91A THR
95A LYS
96A PHE
97A SER
98A HIS
100A GLN
111A ILE
113A PHE
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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
1tvq Details
other holo-structures
pdb ID Ligand Unique ID
1tw4 CHDB1130 CHDB1131 Details
CHDA_130 CHDA_131
2k62 ITLA_202 _YBA_201 Details
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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JN3 NAME: not_found
FORMULA: not_found
SMILES: not_found
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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