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 THR
12 GLY
13 ALA
14 VAL
15 GLY
36 ALA
37 SER
39 ARG
40 SER
43 LYS
56 GLU
57 THR
71 SER
72 ALA
73 GLY
74 SER
75 SER
76 THR
79 LYS
80 TYR
94 ASN
95 THR
96 SER
99 ARG
125 CYS
126 PRO
127 ASN
128 CYS
155 GLN
158 SER
159 GLY
160 ALA
161 GLY
162 MET
163 GLY
166 LEU
189 ILE
209 ILE
210 ASP
220 GLU
223 LYS
245 ARG
252 HIS
325 ASN
326 LEU
329 GLY
330 ALA
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
2gz3 AS2A_400 NAPB_367 56 189 Details
AS2C_400 NAPD_367 56 180
3pwk 25AC_367 27 87 Details
25AL_367 27 86
3q11 NAPG_367 48 114 Details
NAPB_367 48 126
3pws A2PE_368 27 92 Details
A2PC_369 27 88
2gz2 A2PD_501 27 83 Details
A2PB_502 27 85
3pzb 2RAA_367 NAPB_368 55 192 Details
2RAF_367 NAPG_368 55 184
3pyx NAPB_367 48 162 Details
12TI_371 NAPH_367 61 205
2gz1 NAPB_702 48 168 Details
NAPD_701 48 161
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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