3FEG

Crystal structure of human choline kinase beta in complex with phosphorylated hemicholinium-3 and adenosine nucleotide

Structural Biology Knowledgebase: 3FEG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.158

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3FEG

Classification: TRANSFERASE

Total Structure Weight: 45392.34

Macromolecule Entities
Molecule Chains Length Organism Details
Choline/ethanolamine kinase A 379 Homo sapiens EC#: 2.7.1.32 IUBMB 2.7.1.82 IUBMB
Gene Name(s): CHKB Gene View CHETK CHKL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HC7
Query on HC7

A (2S)-2-[4'-({dimethyl[2-(phosphonooxy)ethyl]ammonio}acetyl)biphenyl- 4-yl]-2-hydroxy-4,4-dimethylmorpholin-4-ium
4-dimethylmorpholin-4-ium, (Synonym)
C24 H35 N2 O7 P
MERLSFHNUMSODQ-XMMPIXPASA-P
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ADP
Query on ADP

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AMP
Query on AMP

A ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

A UNKNOWN ATOM OR ION
X
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
HC7 N/A in BindingDB
N/A in BindingMoad
Kd: 45000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.158
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 97.99 α = 90.00
b = 72.99 β = 117.76
c = 62.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-11-29
  • Released Date: 2008-12-23
  • Deposition author(s): Hong, B.S., Tempel, W., Rabeh, W.M., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.W., Structural Genomics Consortium (SGC)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4