4GKR

Structure of the C-terminal motor domain of Kar3 from Candida glabrata

• PDB DOI: https://doi.org/10.2210/pdb4GKR/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Nakaseomyces glabratus CBS 138
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-13 Released: 2012-10-03 
• Deposition Author(s): Duan, D., Allingham, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.257 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 

Literature

Neck Rotation and Neck Mimic Docking in the Noncatalytic Kar3-associated Protein Vik1.

Duan, D., Jia, Z., Joshi, M., Brunton, J., Chan, M., Drew, D., Davis, D., Allingham, J.S.

(2012) J Biol Chem 287: 40292-40301

• PubMed: 23043140 
• DOI: https://doi.org/10.1074/jbc.M112.416529
• Primary Citation of Related Structures:  
  4GKP, 4GKQ, 4GKR


• PubMed Abstract: 
  

  Kar3Vik1 is a heterodimeric kinesin with one catalytic subunit (Kar3) and one noncatalytic subunit (Vik1).

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Organizational Affiliation: 

Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada.

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)

Macromolecule Content

• Total Structure Weight: 84.83 kDa 
• Atom Count: 4,486 
• Modelled Residue Count: 603 
• Deposited Residue Count: 742 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neck and C-terminal motor domain of Kar3	A, B	371	Nakaseomyces glabratus CBS 138	Mutation(s): 0  Gene Names: CAGL0D04994g
UniProt
Find proteins for Q6FVW6 (Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138)) Explore Q6FVW6  Go to UniProtKB:  Q6FVW6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], G [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
EDO	E [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.257 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.707	α = 90
b = 84.066	β = 90
c = 151.127	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Adxv	data processing
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Duan, D., Allingham, J.S.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2012-10-17
  Changes: Database references
• Version 1.2: 2012-12-12
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description