1FBP | pdb_00001fbp

CRYSTAL STRUCTURE OF FRUCTOSE-1,6-BISPHOSPHATASE COMPLEXED WITH FRUCTOSE 6-PHOSPHATE, AMP, AND MAGNESIUM

• PDB DOI: https://doi.org/10.2210/pdb1FBP/pdb

• Classification: HYDROLASE (PHOSPHORIC MONOESTER)
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 1990-05-31 Released: 1992-04-15 
• Deposition Author(s): Ke, H., Zhang, Y., Lipscomb, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.215 (Depositor) 

Literature

Crystal structure of fructose-1,6-bisphosphatase complexed with fructose 6-phosphate, AMP, and magnesium.

Ke, H.M., Zhang, Y.P., Lipscomb, W.N.

(1990) Proc Natl Acad Sci U S A 87: 5243-5247

• PubMed: 2164670 
• DOI: https://doi.org/10.1073/pnas.87.14.5243
• Primary Citation Related Structures: 
  1FBP


• PubMed Abstract: 
  

  The crystal structure of fructose-1,6-bisphosphatase (EC 3.1.3.11) complexed with fructose 6-phosphate, AMP, and Mg2+ has been solved by the molecular replacement method and refined at 2.5-A resolution to a R factor of 0.215, with root-mean-square deviations of 0.013 A and 3.5 degrees for bond lengths and bond angles, respectively. No solvent molecules have been included in the refinement. This structure shows large quaternary and tertiary conformational changes from the structures of the unligated enzyme or its fructose 2,6-bisphosphate complex, but the secondary structures remain essentially the same. Dimer C3-C4 of the enzyme-fructose 6-phosphate-AMP-Mg2+ complex twists about 19 degrees relative to the same dimer of the enzyme-fructose 2,6-bisphosphate complex if their C1-C2 dimers are superimposed on one another. Nevertheless, many interfacial interactions between dimers of C1-C2 and C3-C4 are conserved after quaternary structure changes occur. Residues of the AMP domain (residues 6-200) show large migrations of C alpha atoms relative to barely significant positional changes of the FBP domain (residues 201-335).

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Organizational Affiliation: 
• Gibbs Chemical Laboratory, Harvard University, Cambridge, MA 02138.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 74.27 kDa 
• Atom Count: 4,940 
• Modeled Residue Count: 634 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FRUCTOSE 1,6-BISPHOSPHATASE	A, B	335	Sus scrofa	Mutation(s): 0  EC: 3.1.3.11
UniProt
Find proteins for P00636 (Sus scrofa) Explore P00636  Go to UniProtKB:  P00636

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	E [auth A], H [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
F6P	C [auth A], F [auth B]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.6	α = 90
b = 166.6	β = 90
c = 80	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-04-15 
Deposition Author(s): Ke, H., Zhang, Y., Lipscomb, W.N.

Revision History  

• Version 1.0: 1992-04-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary