6P2D

Structure of mouse ketohexokinase-C in complex with fructose and ADP

• PDB DOI: https://doi.org/10.2210/pdb6P2D/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-21 Released: 2020-06-03 
• Deposition Author(s): Gasper, W.C., Allen, K.N., Tolan, D.R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.220 
• R-Value Work: 0.170 

Literature

Michaelis-like complex of mouse ketohexokinase isoform C

Gasper, W.C., Gardner, S., Ross, A., Oppelt, S.A., Allen, K.N., Tolan, D.R.

(2024) Acta Crystallogr D Biol Crystallogr 

• DOI: https://doi.org/10.1107/S2059798324003723

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 (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.5 kDa 
• Atom Count: 2,726 
• Modelled Residue Count: 296 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketohexokinase	A	315	Mus musculus	Mutation(s): 0  Gene Names: Khk, mCG_23498
UniProt
Find proteins for P97328 (Mus musculus) Explore P97328  Go to UniProtKB:  P97328

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
FRU (Subject of Investigation/LOI)	C [auth A]	beta-D-fructofuranose C6 H12 O6 RFSUNEUAIZKAJO-ARQDHWQXSA-N
NO3	D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.220 
• R-Value Work: 0.170 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.252	α = 90
b = 78.446	β = 90
c = 150.772	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
SADABS	data scaling
PDB_EXTRACT	data extraction
SAINT	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Gasper, W.C., Allen, K.N., Tolan, D.R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.0: 2024-05-29
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary