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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1od0
HYDROLASE HEADER
FAMILY 1 B-GLUCOSIDASE FROM THERMOTOGA MARITIMA TITLE
BETA-GLUCOSIDASE A 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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20 GLN
77 ARG
121 HIS
122 TRP
165 ASN
166 GLU
168 TRP
169 VAL
173 VAL
177 TYR
179 VAL
180 HIS
222 ASN
223 ASN
224 GLY
226 PHE
242 MET
245 PHE
246 ASN
293 ASN
295 TYR
296 SER
298 HIS
312 PHE
322 MET
324 TRP
351 GLU
398 TRP
405 GLU
406 TRP
407 ALA
408 GLU
414 PHE
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
2wc4 AMFA1446 22 83 Details
AMFC1446 22 86
2j7c IDEF1446 22 97 Details
IDEB1446 22 93
2j7g GI4E1446 18 88 Details
GI4B1446 18 80
2wc3 AM3B1446 22 87 Details
AM3A1446 22 86
2jal ACTC1448 YLLA1446 16 81 Details
2wbg LGSA1446 22 91 Details
ACTC1447 LGSB1446 26 122
2j7f GI3F1446 17 74 Details
2cet PGIF1447 22 97 Details
PGIB1447 22 90
2j7d GI1F1446 18 73 Details
GI1C1446 18 73
2j7e GI2F1446 19 79 Details
GI2B1446 19 77
2vrj NCWE1446 22 88 Details
NCWA1446 22 84
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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