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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2v82
LYASE HEADER
KDPGAL COMPLEXED TO KDPGAL TITLE
2-DEHYDRO-3-DEOXY-6-PHOSPHOGALACTONATE 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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KDP B1207
12B ILE
14B ARG
37B GLU
65B GLY
66B THR
85B VAL
86B THR
87B PRO
126B LYS
128B PHE
136A GLN
140A ALA
143A ALA
144A VAL
154B VAL
155B GLY
156B GLY
157B VAL
174B GLY
175B LEU
176B GLY
177B SER
178B ASP
KDP A1207
12A ILE
14A ARG
37A GLU
39A PRO
65A GLY
66A THR
85A VAL
86A THR
87A PRO
126A LYS
128A PHE
136C GLN
140C ALA
143C ALA
144C VAL
154A VAL
155A GLY
156A GLY
157A VAL
174A GLY
175A LEU
176A GLY
177A SER
178A ASP
KDP C1207
12C ILE
14C ARG
37C GLU
39C PRO
65C GLY
66C THR
85C VAL
86C THR
87C PRO
126C LYS
128C PHE
136B GLN
140B ALA
143B ALA
144B VAL
154C VAL
155C GLY
156C GLY
157C VAL
174C GLY
175C LEU
176C GLY
177C SER
178C ASP
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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
2v81 Details
other holo-structures
pdb ID Ligand Unique ID
none
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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KDP NAME: not_found
FORMULA: not_found
SMILES: not_found
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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