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

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

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2bog
HYDROLASE HEADER
CATALYTIC DOMAIN OF ENDO-1,4-GLUCANASE CEL6A MUTANT Y73S FROM THERMOBIFIDA FUSCA IN COMPLEX WITH METHYL CELLOBIOSYL- 4-THIO-BETA-CELLOBIOSIDE TITLE
ENDOGLUCANASE E-2 COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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BGC X 903
41X TRP
73X SER
78X ARG
116X PRO
189X SER
231X TRP
259X LYS
265X ASP
271X ALA
BGC X 904
41X TRP
43X ALA
44X HIS
259X LYS
260X LEU
263X GLU
271X ALA
272X GLY
SGC X 902
41X TRP
116X PRO
117X ASP
121X LEU
159X HIS
162X TRP
188X THR
189X SER
190X ASN
231X TRP
MGL X 901
121X LEU
159X HIS
161X ALA
162X TRP
190X ASN
192X ARG
229X ASN
231X TRP
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:

LigPlot (hosted at the EBI):

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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Hide table of related structures
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List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
2boe Details
other holo-structures
pdb ID Ligand Unique ID
2bof BGCX_901 BGCX_902 BGCX_903 BGCX_904 Details
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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BGC NAME: BETA-D-GLUCOSE
FORMULA: C6 H12 O6
SMILES: OCC1OC(O)C(O)C(O)C1O
MGL NAME: O1-METHYL-GLUCOSE
FORMULA: C7 H14 O6
SMILES: COC1OC(CO)C(O)C(O)C1O
SGC NAME: 4-DEOXY-4-THIO-BETA-D-GLUCOPYRANOSE
FORMULA: C6 H12 O5 S1
SMILES: OCC1OC(O)C(O)C(O)C1S
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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