1BDG | pdb_00001bdg

HEXOKINASE FROM SCHISTOSOMA MANSONI COMPLEXED WITH GLUCOSE

• PDB DOI: https://doi.org/10.2210/pdb1BDG/pdb

• Classification: HEXOKINASE
• Organism(s): Schistosoma mansoni
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-05-08 Released: 1999-05-11 
• Deposition Author(s): Mulichak, A.M., Garavito, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.256 (Depositor) 
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.173 (Depositor) 

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 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.

Macromolecule Content 

• Total Structure Weight: 50.98 kDa 
• Atom Count: 3,481 
• Modeled Residue Count: 444 
• Deposited Residue Count: 451 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEXOKINASE	A	451	Schistosoma mansoni	Mutation(s): 0  EC: 2.7.1.1
UniProt
Find proteins for Q26609 (Schistosoma mansoni) Explore Q26609  Go to UniProtKB:  Q26609

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.256 (Depositor) 
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.3	α = 90
b = 114.3	β = 90
c = 155.2	γ = 120

Software Package:

Software Name	Purpose
R-AXIS	data collection
R-AXIS	data reduction
AMoRE	phasing
X-PLOR	refinement
R-AXIS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-11 
Deposition Author(s): Mulichak, A.M., Garavito, R.M.

Revision History  

• Version 1.0: 1999-05-11
  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: Data collection, Derived calculations, Structure summary
• Version 1.4: 2022-12-21
  Changes: Database references, Structure summary
• Version 1.5: 2023-08-09
  Changes: Refinement description
• Version 1.6: 2024-10-16
  Changes: Data collection, Structure summary