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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2arm
HYDROLASE HEADER
CRYSTAL STRUCTURE OF THE COMPLEX OF PHOSPHOLIPASE A2 WITH A NATURAL COMPOUND ATROPINE AT 1.2 A RESOLUTION TITLE
PHOSPHOLIPASE A2 VRV-PL-VIIIA 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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OIN A 401
2A LEU
5A PHE
28A TYR
29A CYS
30A GLY
31A TRP
32A GLY
45A CYS
48A HIS
49A ASP
52A TYR
53A GLY
68A PRO
69A 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:

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
1fb2 Details
other holo-structures
pdb ID Ligand Unique ID
1kpm VITB_401 Details
2qvd BERA1811 Details
2dpz TYLA2001 Details
1q7a MOHA_125 OPBA_124 Details
1sv9 DIFA_701 Details
1th6 OINA_401 Details
1fv0 9ARE_401 Details
9ARQ_401
3h1x IMNA_301 Details
2b17 DIFA_701 Details
1zwp NIMA_401 Details
2oth IMNA_301 Details
1zyx LCFA2001 Details
1tp2 TDAC_201 Details
TDAE_202
2qhw PZZA_134 Details
3fo7 IMNA_301 Details
3g8f 0PNA_134 Details
2qu9 EUGA_302 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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OIN NAME: (1R,5S)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL (2R)-3-HYDROXY-2-PHENYLPROPANOATE
FORMULA: C17 H23 N1 O3
SMILES: CN1C2CCC1CC(C2)OC(=O)C(CO)c3ccccc3
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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