university lille north of france LigASite database of binding sites

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

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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).

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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.

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21 SER
22 THR
23 ASN
42 GLN
45 GLY
46 HIS
47 GLY
48 ARG
49 LEU
51 ARG
52 LYS
53 TRP
54 GLU
56 PRO
61 TRP
62 LEU
63 SER
100 LYS
102 PRO
103 ASN
104 ASP
106 LEU
111 LYS
112 ILE
114 GLY
115 VAL
116 LEU
127 GLY
128 ILE
129 GLY
131 ASN
134 ASN
135 LYS
136 VAL
137 PRO
139 GLY
140 ALA
227 TYR
231 SER
232 LEU
233 ARG
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:

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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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.

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pdb ID Ligand Unique ID #atoms #contacts
2dth BTNF1402 16 83 Details
BTNC1401 16 81
1x01 ATPE1002 31 106 Details
ATPB1001 31 110
2dkg BT5F1302 38 144 Details
BT5B1301 POPD4001 _MGC1001 48 178
2fyk ADPB1301 BTNC1401 43 163 Details
ADPE1302 BTNF1402 43 155
1wnl ADPE1302 27 96 Details
ADPB1301 27 99
1wqw BT5D1302 38 152 Details
BT5B1301 38 152
2dto ATPB1301 BTNC1401 47 158 Details
ATPE1302 BTNF1402 47 163
2dti BT5F1302 POPH1402 _MNG1502 48 190 Details
BT5B1301 POPD1401 _MNC1501 48 184
1wpy BTNB1301 16 80 Details
BTND1302 16 82
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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