university lille north of france LigASite database of binding sites
apo-structureHelp

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

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2bgk
OXIDOREDUCTASE HEADER
X-RAY STRUCTURE OF APO-SECOISOLARICIRESINOL DEHYDROGENASE TITLE
RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE COMPND
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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22 THR
23 GLY
25 ALA
26 GLY
27 GLY
28 ILE
29 GLY
46 ALA
47 ASP
48 ILE
49 ALA
71 CYS
72 ASP
73 VAL
74 THR
99 ASN
100 VAL
101 GLY
102 VAL
103 LEU
104 SER
106 THR
124 ILE
151 THR
152 ALA
153 SER
154 ILE
155 SER
162 GLY
163 VAL
164 SER
167 TYR
171 LYS
197 PRO
198 TYR
199 ILE
200 VAL
201 ALA
202 SER
203 PRO
216 VAL
262 TYR
266 ASN
269 PHE
270 PRO
273 LEU
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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holo-structuresHelp

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
2bgl NAJF1300 44 170 Details
NAJB1300 44 170
NAJH1300 44 176
NAJD1300 44 176
2bgm MAXE6001 NAJF1300 70 248 Details
MAXB6001 NAJC1300 70 248
MAXH6001 NAJI1300 70 248
MAXK6001 NAJL1300 70 248
v9.7
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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