1BG3

RAT BRAIN HEXOKINASE TYPE I COMPLEX WITH GLUCOSE AND INHIBITOR GLUCOSE-6-PHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb1BG3/pdb

• Classification: HEXOKINASE
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 1998-06-04 Released: 1999-06-08 
• Deposition Author(s): Mulichak, A.M., Garavito, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

The structure of mammalian hexokinase-1.

Mulichak, A.M., Wilson, J.E., Padmanabhan, K., Garavito, R.M.

(1998) Nat Struct Biol 5: 555-560

• PubMed: 9665168 
• DOI: https://doi.org/10.1038/811
• Primary Citation of Related Structures:  
  1BDG, 1BG3


• PubMed Abstract: 
  

  We have determined the structures of the glucose-6-phosphate (G6P)-inhibitable 100,000 Mr Type I hexokinase from rat and the G6P-sensitive 50,000 Mr hexokinase from Schistosoma mansoni at a resolution of 2.8 and 2.6 A respectively. The structures define the glucose and G6P binding sites in these enzymes, suggest the mechanisms of intradomain G6P inhibition and activity loss in the Type I hexokinase N-terminal half, and reveal the structure of the membrane targeting motif that integrates the Type I hexokinase into the outer mitochondrial membrane.

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Organizational Affiliation: 

Department of Biochemistry, Michigan State University, East Lansing, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 206.89 kDa 
• Atom Count: 13,962 
• Modelled Residue Count: 1,804 
• Deposited Residue Count: 1,836 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEXOKINASE	A, B	918	Rattus norvegicus	Mutation(s): 0  EC: 2.7.1.1
UniProt
Find proteins for P05708 (Rattus norvegicus) Explore P05708  Go to UniProtKB:  P05708

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G6P	D [auth A], F [auth A], I [auth B], K [auth B]	6-O-phosphono-alpha-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-DVKNGEFBSA-N
BGC	C [auth A], E [auth A], H [auth B], J [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.1	α = 90
b = 77.1	β = 96
c = 137.1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
R-AXIS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-08 
Deposition Author(s): Mulichak, A.M., Garavito, R.M.

Revision History  

• Version 1.0: 1999-06-08
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Structure summary
• Version 1.5: 2024-04-03
  Changes: Refinement description