university lille north of france LigASite database of binding sites

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

(click anywhere in this window to remove it)
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

(click anywhere in this window to remove it)
Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

(click anywhere in this window to remove it)
10 LEU
17 LEU
18 ALA
19 ILE
21 TYR
22 TYR
23 SER
27 TYR
28 TYR
29 CYS
30 GLY
31 TRP
32 GLY
33 GLY
43 ARG
44 CYS
45 CYS
46 PHE
47 VAL
48 HIS
49 ASP
50 CYS
51 TYR
52 TYR
53 GLY
54 ASN
55 LEU
56 PRO
59 PRO
60 LYS
61 CYS
67 ASN
68 PRO
69 LYS
96 PHE
106 PHE
129 GLU
130 LEU
133 CYS
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.

(click anywhere in this window to remove it)

Links to external databases:

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.

(click anywhere in this window to remove it)

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

(click anywhere in this window to remove it)
pdb ID Ligand Unique ID #atoms #contacts
1kpm VITB_401 31 148 Details
2qvd BERA1811 25 96 Details
2dpz TYLA2001 11 78 Details
1q7a MOHA_125 OPBA_124 26 111 Details
1sv9 DIFA_701 19 103 Details
1th6 OINA_401 21 86 Details
1fv0 9ARE_401 26 124 Details
9ARQ_401 26 123
3h1x IMNA_301 25 83 Details
2b17 DIFA_701 19 104 Details
1zwp NIMA_401 21 77 Details
2oth IMNA_301 25 85 Details
1zyx LCFA2001 27 103 Details
2arm OINA_401 21 85 Details
1tp2 TDAC_201 15 91 Details
TDAE_202 15 91
2qhw PZZA_134 17 70 Details
3fo7 IMNA_301 25 87 Details
3g8f 0PNA_134 40 121 Details
2qu9 EUGA_302 11 72 Details
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
Script execution time: 0.0743 seconds