5ZQT | pdb_00005zqt

Crystal structure of Oryza sativa hexokinase 6

• PDB DOI: https://doi.org/10.2210/pdb5ZQT/pdb

• Classification: TRANSFERASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-20 Released: 2019-04-24 
• Deposition Author(s): Matsudaira, K., Mochizuki, S., Yoshida, H., Kamitori, S., Akimitsu, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 
  0.266 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Oryza sativa hexokinase 6

Matsudaira, K., Mochizuki, S., Yoshida, H., Kamitori, S., Akimitsu, K.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 157.73 kDa 
• Atom Count: 10,736 
• Modeled Residue Count: 1,368 
• Deposited Residue Count: 1,419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexokinase-6	A, B, C	473	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: HXK6, HXK2, Os01g0742500, LOC_Os01g53930, P0439E07.19 EC: 2.7.1.1
UniProt
Find proteins for Q8LQ68 (Oryza sativa subsp. japonica) Explore Q8LQ68  Go to UniProtKB:  Q8LQ68

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	D [auth A], G [auth B], J [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
BGC (Subject of Investigation/LOI)	F [auth A], I [auth B], L [auth C]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
MG (Subject of Investigation/LOI)	E [auth A], H [auth B], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free:  0.266 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.6	α = 90
b = 131.6	β = 90
c = 188.92	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Matsudaira, K., Mochizuki, S., Yoshida, H., Kamitori, S., Akimitsu, K.

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary