3F2R

Crystal structure of human choline kinase alpha in complex with hemicholinium-3

• PDB DOI: https://doi.org/10.2210/pdb3F2R/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-10-30 Released: 2008-11-11 
• Deposition Author(s): Hong, B., Tempel, W., Rabeh, W.M., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.275 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

Crystal structure of human choline kinase alpha in complex with hemicholinium-3

Hong, B., Tempel, W., Rabeh, W.M., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

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)

Macromolecule Content

• Total Structure Weight: 94.54 kDa 
• Atom Count: 5,455 
• Modelled Residue Count: 654 
• Deposited Residue Count: 802 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline kinase alpha	A, B	401	Homo sapiens	Mutation(s): 3  Gene Names: CHKA, CHK, CKI EC: 2.7.1.32 (PDB Primary Data), 2.7.1.82 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P35790 (Homo sapiens) Explore P35790  Go to UniProtKB:  P35790
PHAROS:  P35790 GTEx:  ENSG00000110721

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HC6	C [auth A], F [auth B]	(2S,2'S)-2,2'-biphenyl-4,4'-diylbis(2-hydroxy-4,4-dimethylmorpholin-4-ium) C24 H34 N2 O4 JIWUESGGKYLPPG-DNQXCXABSA-N
UNX	D [auth A], E [auth A], G [auth B], H [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.275 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.553	α = 90
b = 119.581	β = 90
c = 131.301	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
Coot	model building
MolProbity	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-11 
Deposition Author(s): Hong, B., Tempel, W., Rabeh, W.M., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-11-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2020-10-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2023-09-06
  Changes: Data collection, Database references, Refinement description