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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1lic
LIPID-BINDING PROTEIN HEADER
X-RAY CRYSTALLOGRAPHIC STRUCTURES OF ADIPOCYTE LIPID BINDING PROTEIN COMPLEXED WITH PALMITATE AND HEXADECANESULFONIC ACID. PROPERTIES OF CAVITY BINDING SITES. TITLE
ADIPOCYTE LIPID-BINDING PROTEIN 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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HDS A 133
16A PHE
19A TYR
20A MET
23A VAL
25A VAL
29A THR
32A VAL
33A ALA
36A ALA
38A PRO
40A MET
53A SER
55A SER
57A PHE
58A LYS
74A THR
75A ALA
76A ASP
78A ARG
95A GLN
104A ILE
106A ARG
115A VAL
126A ARG
128A TYR
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
1lib Details
other holo-structures
pdb ID Ligand Unique ID
1adl ACDI_135 __OK_133 __OL_132 __OJ_134 Details
ACDC_135 __OF_132 __OE_133 __OD_134
1lid OLAA_132 Details
3hk1 B64A_132 Details
1lif STEA_132 Details
1lie PLMA_133 Details
2ans 2ANB_201 Details
2ANE_202
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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HDS NAME: 1-HEXADECANOSULFONIC ACID
FORMULA: C16 H34 O3 S1
SMILES: CCCCCCCCCCCCCCCCS(O)(=O)=O
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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