1NUH

The crystal structure of human phosphoglucose isomerase complexed with 5-phosphoarabinonate

• PDB DOI: https://doi.org/10.2210/pdb1NUH/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-01-31 Released: 2003-02-11 
• Deposition Author(s): Davies, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.268 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Starting Model: experimental

Literature

The structure of human phosphoglucose isomerase complexed with a transition-state analogue.

Davies, C., Muirhead, H., Chirgwin, J.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1111-1113

• PubMed: 12777791 
• DOI: https://doi.org/10.1107/s0907444903007352
• Primary Citation of Related Structures:  
  1NUH


• PubMed Abstract: 
  

  Phosphoglucose isomerase (PGI) is a workhorse enzyme of carbohydrate metabolism that interconverts glucose 6-phosphate and fructose 6-phosphate. Outside the cell, however, the protein appears to function as a cytokine. A crystal structure of human PGI bound with 5-phosphoarabinonate, a strong inhibitor that mimics the cis-enediol(ate) intermediate of the reaction, has been determined at 2.5 A resolution. The structure helps to confirm the assignment of Glu357 as the base catalyst in the isomerase reaction.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 64.05 kDa 
• Atom Count: 4,578 
• Modelled Residue Count: 555 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glucose phosphate isomerase	A	558	Homo sapiens	Mutation(s): 0  Gene Names: GPI EC: 5.3.1.9
UniProt & NIH Common Fund Data Resources
Find proteins for P06744 (Homo sapiens) Explore P06744  Go to UniProtKB:  P06744
GTEx:  ENSG00000105220

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PA5	H [auth A]	5-PHOSPHOARABINONIC ACID C5 H11 O9 P HNECGPFIYSOYHF-JJYYJPOSSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.268 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.4	α = 90
b = 94.4	β = 90
c = 137.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-11 
Deposition Author(s): Davies, C.

Revision History  

• Version 1.0: 2003-02-11
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description