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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11 GLU
12 TYR
13 HIS
14 ASN
31 LEU
32 ALA
33 GLY
34 LYS
35 ARG
51 GLU
53 PRO
54 GLY
55 SER
56 GLN
57 HIS
58 ILE
59 ASP
60 SER
61 GLN
62 LYS
88 TRP
90 ASN
91 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:

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
1rd9 BV2D_105 37 98 Details
BV2F_106 24 72
BV2I_108 37 109
BV2B_104 24 75
1pzj J15J_106 37 106 Details
J15H_105 37 106
1eei GAAH_506 21 71 Details
GAAD_508 21 73
GAAJ_507 21 71
GAAB_504 21 72
1pzk J12J_104 21 71 Details
J12F_106 21 70
J12H_107 21 71
J12D_108 37 109
1md2 233F2201 233G2203 _SQV2202 49 133 Details
233R2201 233S2203 _SQW2202 49 141
233T1204 _SQY1205 233U1206 59 154
233M1207 CYNO1208 233N1207 50 114
233H1204 233I1206 _SQX1205 59 154
1rdp BV3L_108 24 76 Details
BV3J_107 24 76
BV3B_104 24 73
BV3G_106 24 73
1rcv BV1B_104 24 75 Details
BV1J_105 36 95
1llr FNGN_104 LNQO_105 45 126 Details
FNGK_104 LNQL_105 45 107
FNGE_104 LNQF_105 45 119
FNGH_104 LNQI_105 45 112
FNGB_104 LNQC_105 45 122
1rf2 BV4L_108 24 75 Details
BV4J_107 24 73
BV4G_106 24 77
BV4B_104 24 82
1jr0 A24E_104 32 86 Details
A24O_104 32 84
A24B_104 32 79
A24L_104 32 82
A24H_104 32 85
A24Q_104 32 84
A24J_104 32 99
A24R_104 32 91
A24T_104 32 100
A24G_104 32 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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