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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1phw
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE ANALOG 1-DEOXY-A5P 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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N D 70
1062C ASN
1095C ASP
1113C GLN
1115C PRO
1116C ALA
1117C PHE
1120G ARG
1138C LYS
1141C GLN
1168C ARG
1202C HIS
1251C GLY
1252C PRO
N H 70
1062G ASN
1095G ASP
1113G GLN
1115G PRO
1116G ALA
1117G PHE
1120C ARG
1138G LYS
1141G GLN
1168G ARG
1202G HIS
1251G GLY
1252G PRO
N F 70
1062E ASN
1095E ASP
1113E GLN
1115E PRO
1116E ALA
1117E PHE
1120A ARG
1138E LYS
1141E GLN
1168E ARG
1202E HIS
1251E GLY
1252E PRO
N B 70
1062A ASN
1095A ASP
1113A GLN
1115A PRO
1116A ALA
1117A PHE
1120E ARG
1138A LYS
1141A GLN
1168A ARG
1202A HIS
1251A GLY
1252A 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
1x6u DO8H2634 Details
DO8B2634
DO8F2634
DO8D2634
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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N NAME: ANY 5'-MONOPHOSPHATE NUCLEOTIDE
FORMULA: C5 H11 O7 P1
SMILES: OC1COC(COP(O)(O)=O)C1O
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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