6UL7 | pdb_00006ul7

Structure of human ketohexokinase-C in complex with fructose, NO3, and osthole

• PDB DOI: https://doi.org/10.2210/pdb6UL7/pdb

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


• Deposited: 2019-10-07 Released: 2021-04-07 
• Deposition Author(s): Gasper, W.C., Gardner, S., Allen, K.N., Tolan, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.231 (DCC) 

Starting Model: experimental

Literature

Structure of human ketohexokinase-C in complex with fructose, NO3, and osthole

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.22 kDa 
• Atom Count: 2,509 
• Modeled Residue Count: 297 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketohexokinase	A	318	Homo sapiens	Mutation(s): 0  Gene Names: KHK EC: 2.7.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P50053 (Homo sapiens) Explore P50053  Go to UniProtKB:  P50053
PHAROS:  P50053 GTEx:  ENSG00000138030

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A0O (Subject of Investigation/LOI)	C [auth A]	7-methoxy-8-(3-methylbut-2-enyl)chromen-2-one C15 H16 O3 MBRLOUHOWLUMFF-UHFFFAOYSA-N
FRU	B [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: 2.30 Å
• R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.231 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.87	α = 90
b = 106.87	β = 90
c = 79.03	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Gasper, W.C., Gardner, S., Allen, K.N., Tolan, D.R.

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description