4L3Q

Crystal structure of glucokinase-activator complex

• PDB DOI: https://doi.org/10.2210/pdb4L3Q/pdb

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


• Deposited: 2013-06-06 Released: 2013-07-24 
• Deposition Author(s): Gajiwala, K.S., Filipski, K.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.304 
• R-Value Work: 0.254 
• R-Value Observed: 0.259 

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: 51.63 kDa 
• Atom Count: 3,537 
• Modelled Residue Count: 447 
• Deposited Residue Count: 457 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	457	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
926	C [auth A]	6-{3-[(1-methyl-1H-imidazol-2-yl)sulfanyl]phenyl}pyridin-2(1H)-one C15 H13 N3 O S YYWBGPHQPMDZEM-UHFFFAOYSA-N
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
926	BindingDB:  4L3Q	EC50: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.304 
• R-Value Work: 0.254 
• R-Value Observed: 0.259 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.512	α = 90
b = 79.512	β = 90
c = 321.131	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Gajiwala, K.S., Filipski, K.J.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2013-08-07
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary