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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1adl
LIPID-BINDING PROTEIN HEADER
ADIPOCYTE LIPID BINDING PROTEIN COMPLEXED WITH ARACHIDONIC ACID: X-RAY CRYSTALLOGRAPHIC AND TITRATION CALORIMETRY STUDIES 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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ACD I 135
16G PHE
19G TYR
20G MET
23G VAL
25G VAL
29G THR
32G VAL
33G ALA
36G ALA
38G PRO
53G SER
55G SER
57G PHE
58G LYS
60G THR
74G THR
75G ALA
76G ASP
78G ARG
95G GLN
104G ILE
106G ARG
115G VAL
117G CYS
126G ARG
128G TYR
O K 133
16G PHE
115G VAL
116G GLU
117G CYS
124G SER
126G ARG
O J 134
16G PHE
19G TYR
104G ILE
117G CYS
ACD C 135
16A PHE
19A TYR
20A MET
23A VAL
25A VAL
29A THR
32A VAL
33A ALA
36A ALA
38A PRO
53A SER
55A SER
57A PHE
58A LYS
60A THR
74A THR
75A ALA
76A ASP
78A ARG
95A GLN
104A ILE
106A ARG
115A VAL
117A CYS
126A ARG
128A TYR
O E 133
16A PHE
115A VAL
116A GLU
117A CYS
124A SER
126A ARG
O D 134
16A PHE
19A TYR
104A ILE
117A CYS
O L 132
40G MET
106G ARG
115G VAL
128G TYR
O F 132
40A MET
106A ARG
115A VAL
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
1lid OLAA_132 Details
3hk1 B64A_132 Details
1lif STEA_132 Details
1lic HDSA_133 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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ACD NAME: ARACHIDONIC ACID
FORMULA: C20 H32 O2
SMILES: CCCCCC=CCC=CCC=CCC=CCCCC(O)=O
O NAME: OXYGEN ATOM
FORMULA: O1
SMILES: 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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