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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10 GLY
11 GLY
12 ASP
21 ARG
25 ARG
41 TYR
54 ARG
55 TYR
57 VAL
58 SER
59 ASP
60 MET
61 ILE
71 ALA
72 ARG
73 PHE
74 PRO
76 PHE
77 ARG
82 ARG
102 GLY
103 ASP
104 GLY
105 SER
107 MET
108 GLY
111 ARG
124 GLY
125 THR
126 ILE
127 ASP
129 ASP
154 ARG
158 SER
162 ARG
169 MET
170 GLY
171 ARG
185 GLY
186 CYS
187 GLU
211 LYS
212 GLY
213 LYS
214 LYS
215 HIS
222 GLU
223 HIS
243 ARG
249 HIS
252 ARG
319 TYR
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
1pfk ADPU_324 _MGW_325 FBPV_323 48 200 Details
ADPB_326 _MGF_327 28 111
ADPT_326 _MGX_327 28 112
ADPC_324 FBPD_323 _MGE_325 48 209
ADPI_324 FBPJ_323 _MGK_325 48 203
ADPN_326 _MGR_327 28 112
ADPH_326 _MGL_327 28 117
ADPO_324 FBPP_323 _MGQ_325 48 208
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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