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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3cxi
TOXIN HEADER
STRUCTURE OF BTHTX-I COMPLEXED WITH ALPHA-TOCOPHEROL TITLE
MYOTOXIC PHOSPHOLIPASE A2-LIKE 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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VIT B 311
2B LEU
3B PHE
5B LEU
6B GLY
7B LYS
9B ILE
10B LEU
18B PRO
19B ALA
22B TYR
23B GLY
28B ASN
29B CYS
30B GLY
31A VAL
32A LEU
45B CYS
48B HIS
49B LYS
52B TYR
68B PRO
69B LYS
102B VAL
106B LEU
121A LEU
122A LYS
123A PRO
VIT A 306
2A LEU
3A PHE
5A LEU
6A GLY
7A LYS
9A ILE
10A LEU
17A ASN
18A PRO
19A ALA
22A TYR
23A GLY
29A CYS
30A GLY
31A VAL
45A CYS
48A HIS
49A LYS
52A TYR
69A LYS
121B LEU
122B LYS
123B PRO
PE4 B 310
4B GLU
7B LYS
10B LEU
11B GLN
15B GLY
75B TYR
76B SER
77B TRP
121A LEU
123A PRO
125A 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
Help

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
3i3i Details
other holo-structures
pdb ID Ligand Unique ID
3i03 IPAA_211 PBPA_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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PE4 NAME: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
FORMULA: C16 H34 O8
SMILES: CCOCCOCCOCCOCCOCCOCCOCCO
VIT NAME: VITAMIN E
FORMULA: C29 H50 O2
SMILES: CC(C)CCCC(C)CCCC(C)CCCC1(C)CCc2c(C)c(O)c(C)c(C)c2O1
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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