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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4ald
LYASE HEADER
HUMAN MUSCLE FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE COMPLEXED WITH FRUCTOSE 1,6-BISPHOSPHATE TITLE
FRUCTOSE-BISPHOSPHATE 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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2FP H 364
31G ALA
33G ASP
34G GLU
35G SER
38G SER
42G ARG
77G ILE
107G LYS
146G LYS
148G ARG
187G GLU
189G GLU
229G LYS
270G LEU
271G SER
272G GLY
273G GLY
300G SER
301G TYR
302G GLY
303G ARG
2FP B 364
31A ALA
33A ASP
34A GLU
35A SER
38A SER
42A ARG
77A ILE
107A LYS
146A LYS
148A ARG
187A GLU
189A GLU
229A LYS
270A LEU
271A SER
272A GLY
273A GLY
300A SER
301A TYR
302A GLY
303A ARG
2FP F 364
31E ALA
33E ASP
34E GLU
35E SER
38E SER
42E ARG
77E ILE
107E LYS
146E LYS
148E ARG
187E GLU
189E GLU
229E LYS
270E LEU
271E SER
272E GLY
273E GLY
300E SER
301E TYR
302E GLY
303E ARG
2FP D 364
31C ALA
33C ASP
34C GLU
35C SER
38C SER
42C ARG
77C ILE
107C LYS
146C LYS
148C ARG
187C GLU
189C GLU
229C LYS
270C LEU
271C SER
272C GLY
273C GLY
300C SER
301C TYR
302C GLY
303C ARG
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
2ald 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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2FP NAME: 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)
FORMULA: C6 H14 O12 P2
SMILES: OC(COP(O)(O)=O)C(O)C(O)C(=O)COP(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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