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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1lby
HYDROLASE HEADER
CRYSTAL STRUCTURE OF A COMPLEX (P32 CRYSTAL FORM) OF DUAL ACTIVITY FBPASE/IMPASE (AF2372) FROM ARCHAEOGLOBUS FULGIDUS WITH 3 MANGANESE IONS, FRUCTOSE-6-PHOSPHATE, AND PHOSPHATE ION TITLE
FRUCTOSE 1,6-BISPHOSPHATASE/INOSITOL 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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MN C 292
38A ASP
40A THR
41A PRO
46A ASP
67A GLU
68A GLU
PO4 B 293
40A THR
46A ASP
67A GLU
86A GLY
87A THR
88A PHE
MN E 291
46A ASP
67A GLU
68A GLU
82A ASP
84A LEU
85A ASP
87A THR
F6P L 295
67A GLU
85A ASP
86A GLY
155A TYR
156A TYR
170A GLY
171A SER
172A ALA
175A GLU
189A ASP
191A ARG
195A MET
196A LEU
197A ARG
200A ASP
465G ARG
467G ARG
MN F 290
67A GLU
82A ASP
85A ASP
200A ASP
F6P D 595
164A LYS
165A ARG
167A ARG
385G ASP
455G TYR
456G TYR
470G GLY
471G SER
472G ALA
489G ASP
491G ARG
496G LEU
500G ASP
MN I 592
338G ASP
340G THR
341G PRO
346G ASP
367G GLU
368G GLU
PO4 H 593
346G ASP
367G GLU
382G ASP
384G LEU
385G ASP
386G GLY
387G THR
388G PHE
MN J 591
346G ASP
367G GLU
368G GLU
382G ASP
383G PRO
384G LEU
387G THR
MN K 590
367G GLU
382G ASP
385G ASP
499G TYR
500G 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
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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
1lbv Details
other holo-structures
pdb ID Ligand Unique ID
1lbx IPDD_295 _CAB_291 _CAC_290 Details
IPDH_595 _CAG_591 _CAF_590
1lbz FBPJ_595 _CAI_590 _CAH_591 Details
FBPE_295 _CAD_290 _CAC_291
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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F6P NAME: FRUCTOSE-6-PHOSPHATE
FORMULA: C6 H13 O9 P1
SMILES: OCC1(O)OC(COP(O)(O)=O)C(O)C1O
PO4 NAME: PHOSPHATE ION
FORMULA: O4 P1
SMILES: [O-]P([O-])([O-])=O
MN NAME: MANGANESE (II) ION
FORMULA: MN1
SMILES: [Mn++]
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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