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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2ot1
LYASE HEADER
FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM RABBIT MUSCLE IN COMPLEX WITH NAPHTHOL AS-E PHOSPHATE, A COMPETITIVE INHIBITOR TITLE
FRUCTOSE-BISPHOSPHATE ALDOLASE A 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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N3P D3004
34C GLU
38C SER
39C ILE
42C ARG
58C TYR
272C GLY
302C GLY
303C ARG
306C GLN
307C ALA
310C LEU
N3P B3001
34A GLU
38A SER
39A ILE
42A ARG
58A TYR
272A GLY
302A GLY
303A ARG
306A GLN
307A ALA
310A LEU
N3P F3002
34E GLU
38E SER
41E LYS
42E ARG
58E TYR
237E HIS
272E GLY
273E GLY
302E GLY
303E ARG
306E GLN
307E ALA
310E LEU
N3P H3003
34G GLU
38G SER
39G ILE
42G ARG
58G TYR
272G GLY
302G GLY
303G ARG
306G GLN
307G ALA
310G LEU
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
1zah Details
other holo-structures
pdb ID Ligand Unique ID
3tu9 5MMB_364 Details
5MMF_364
1zaj M2PF3003 Details
M2PH3004
M2PB3001
M2PD3002
1zai 2FPH3003 Details
2FPD3004
2FPB3001
2FPF3002
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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N3P 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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