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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1g7v
LYASE HEADER
CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEXES WITH THE MECHANISM-BASED INHIBITOR 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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PAI D 300
26C ASN
27C VAL
60C LYS
62C ASN
63C ARG
64C SER
68C SER
69C TYR
115C PRO
116C ALA
117C PHE
138C LYS
141C GLN
142G PHE
168C ARG
175C ASP
177C LEU
202C HIS
205C GLN
206C CYS
246C HIS
247C ALA
250C ASP
251C GLY
252C PRO
PAI B 300
26A ASN
27A VAL
60A LYS
62A ASN
63A ARG
64A SER
68A SER
69A TYR
115A PRO
116A ALA
117A PHE
138A LYS
141A GLN
142E PHE
168A ARG
175A ASP
177A LEU
202A HIS
205A GLN
206A CYS
246A HIS
247A ALA
250A ASP
251A GLY
252A PRO
PAI H 300
26G ASN
27G VAL
60G LYS
62G ASN
63G ARG
64G SER
68G SER
69G TYR
115G PRO
116G ALA
117G PHE
138G LYS
141G GLN
142C PHE
168G ARG
175G ASP
177G LEU
202G HIS
205G GLN
206G CYS
246G HIS
247G ALA
250G ASP
251G GLY
252G PRO
PAI F 300
26E ASN
27E VAL
60E LYS
62E ASN
63E ARG
64E SER
68E SER
69E TYR
115E PRO
116E ALA
117E PHE
138E LYS
141E GLN
142A PHE
168E ARG
175E ASP
177E LEU
202E HIS
205E GLN
206E CYS
246E HIS
247E ALA
250E ASP
251E GLY
252E 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
Help

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).

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apo-structure
pdb ID
1x8f Details
other holo-structures
pdb ID Ligand Unique ID
1x6u DO8H2634 Details
DO8B2634
DO8F2634
DO8D2634
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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PAI NAME: {[(2,2-DIHYDROXY-ETHYL)-(2,3,4,5-TETRAHYDROXY-6-PHOSPHONOOXY-HEXYL)-AMINO]-METHYL}-PHOSPHONIC ACID
FORMULA: C9 H23 N1 O13 P2
SMILES: OC(O)CN(CC(O)C(O)C(O)C(O)COP(O)(O)=O)CP(O)(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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