2JBV

Crystal structure of choline oxidase reveals insights into the catalytic mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.169

Literature

Macromolecules
Sequence Display for 2JBV

Classification: OXIDOREDUCTASE

Total Structure Weight: 121532.94

Macromolecule Entities
Molecule Chains Length Organism Details
CHOLINE OXIDASE A, B 546 Arthrobacter globiformis EC#: 1.1.3.17 IUBMB
Details: COVALENT LINKAGE BETWEEN C8M ATOM OF FAO AND NE2 ATOM OF HIS99 OF CHOLINE OXIDASE
Gene Name(s): codA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)- 3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)- 5-[(4aS,10aR)-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a- hexahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4- trihydroxypentyl dihydrogen diphosphate
C27 H37 N9 O15 P2
VSWYNLHGQAGAHX-AWYOOINRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A, B DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

A, B UNKNOWN ATOM OR ION
X
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
FAO N/A in BindingDB
N/A in BindingMoad
Kd: 290000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.169
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 84.36 α = 90.00
b = 84.36 β = 90.00
c = 343.45 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-12-13
  • Released Date: 2007-12-25
  • Deposition author(s): Lountos, G.T., Fan, F., Gadda, G., Orville, A.M.

Revision History

  • Version 1_0: 2007-12-25

    Type: Initial release

  • Version 1_1: 2011-05-08

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance