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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1x8f
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF APO-KDO8P SYNTHASE TITLE
2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE 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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26 ASN
27 VAL
55 LYS
57 SER
60 LYS
62 ASN
63 ARG
64 SER
68 SER
69 TYR
94 THR
95 ASP
97 HIS
113 GLN
115 PRO
116 ALA
117 PHE
118 LEU
121 GLN
138 LYS
141 GLN
142 PHE
168 ARG
175 ASP
177 LEU
199 ASP
201 THR
202 HIS
205 GLN
206 CYS
237 PHE
239 GLU
246 HIS
247 ALA
250 ASP
251 GLY
252 PRO
1062 ASN
1095 ASP
1113 GLN
1115 PRO
1116 ALA
1117 PHE
1120 ARG
1138 LYS
1141 GLN
1168 ARG
1202 HIS
1251 GLY
1252 PRO
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
1g7v PAID_300 25 116 Details
PAIB_300 25 116
PAIH_300 25 113
PAIF_300 25 113
1x6u DO8H2634 20 89 Details
DO8B2634 20 89
DO8F2634 20 95
DO8D2634 20 95
1phw __ND__70 13 74 Details
__NH__70 13 74
__NF__70 13 74
__NB__70 13 74
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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