4FPA

Crystal Structure of recombinant human Hexokinase type I mutant D413N Glucose 6-Phosphate

• PDB DOI: https://doi.org/10.2210/pdb4FPA/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-06-21 Released: 2013-07-03 
• Deposition Author(s): Shen, L., Honzatko, R.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.256 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 

Literature

DETERMINATION OF SITE AFFINITY CONSTANTS FOR PRODUCT INHIBITION of WILD-TYPE AND MUTANT FORMS OF RECOMBINANT HUMAN HEXOKINASE TYPE I

Shen, L., Gao, Y., Honzatko, R.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 207.49 kDa 
• Atom Count: 14,391 
• Modelled Residue Count: 1,798 
• Deposited Residue Count: 1,834 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexokinase-1	A, B	917	Homo sapiens	Mutation(s): 1  Gene Names: HK1 EC: 2.7.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P19367 (Homo sapiens) Explore P19367  Go to UniProtKB:  P19367
PHAROS:  P19367 GTEx:  ENSG00000156515

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BG6	D [auth A], F [auth A], K [auth B], M [auth B]	6-O-phosphono-beta-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-VFUOTHLCSA-N
CIT	I [auth A], P [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
BGC	C [auth A], E [auth A], J [auth B], L [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
NA	G [auth A], H [auth A], N [auth B], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.256 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.607	α = 90
b = 121.14	β = 92.69
c = 119.888	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Shen, L., Honzatko, R.B.

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Structure summary