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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1x6u
TRANSFERASE HEADER
KDO8P SYNTHASE IN IT'S BINARY COMPLEX WITH THE PRODUCT KDO8P TITLE
2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE 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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DO8 H2634
26G ASN
55G LYS
57G SER
60G LYS
62G ASN
63G ARG
95G ASP
97G HIS
113G GLN
115G PRO
116G ALA
117G PHE
118G LEU
121C GLN
138G LYS
199G ASP
201G THR
202G HIS
237G PHE
239G GLU
252G PRO
DO8 B2634
26A ASN
55A LYS
57A SER
60A LYS
62A ASN
63A ARG
95A ASP
97A HIS
113A GLN
115A PRO
116A ALA
117A PHE
118A LEU
121E GLN
138A LYS
199A ASP
201A THR
202A HIS
237A PHE
239A GLU
252A PRO
DO8 F2634
26E ASN
55E LYS
57E SER
60E LYS
62E ASN
63E ARG
94E THR
95E ASP
97E HIS
113E GLN
115E PRO
116E ALA
117E PHE
118E LEU
121A GLN
138E LYS
199E ASP
201E THR
202E HIS
237E PHE
239E GLU
252E PRO
DO8 D2634
26C ASN
55C LYS
57C SER
60C LYS
62C ASN
63C ARG
94C THR
95C ASP
97C HIS
113C GLN
115C PRO
116C ALA
117C PHE
118C LEU
121G GLN
138C LYS
199C ASP
201C THR
202C HIS
237C PHE
239C GLU
252C 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:

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
1x8f Details
other holo-structures
pdb ID Ligand Unique ID
1g7v PAID_300 Details
PAIB_300
PAIH_300
PAIF_300
1phw __ND__70 Details
__NH__70
__NF__70
__NB__70
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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DO8 NAME: 3-DEOXY-D-MANNO-2-OCTULOSONATE-8-PHOSPHATE
FORMULA: C8 H15 O11 P1
SMILES: OC(COP(O)(O)=O)C1OC(O)(CC(O)C1O)C(O)=O
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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