5V4X

Human glucokinase in complex with novel pyrazole activator.

• PDB DOI: https://doi.org/10.2210/pdb5V4X/pdb

• Classification: transferase/transferase activator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-10 Released: 2017-05-31 
• Deposition Author(s): Skene, R.J., Hosfiled, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.250 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 52.42 kDa 
• Atom Count: 3,551 
• Modelled Residue Count: 420 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	458	Homo sapiens	Mutation(s): 0  Gene Names: GCK EC: 2.7.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for P35557 (Homo sapiens) Explore P35557  Go to UniProtKB:  P35557
PHAROS:  P35557 GTEx:  ENSG00000106633

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8WJ	C [auth A]	(2S)-3-cyclohexyl-2-[4-(cyclopentylsulfonyl)-2-oxopyridin-1(2H)-yl]-N-(1,3-thiazol-2-yl)propanamide C22 H29 N3 O4 S2 AIIAMUOQMJYEJH-IBGZPJMESA-N
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
IOD	D [auth A], E [auth A], F [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.250 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.874	α = 90
b = 77.855	β = 90
c = 119.927	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Skene, R.J., Hosfiled, D.J.

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-03-06
  Changes: Data collection, Database references, Structure summary