3VSJ

Crystal structure of 1,6-APD (2-ANIMOPHENOL-1,6-DIOXYGENASE) complexed with intermediate products

Structural Biology Knowledgebase: 3VSJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VSJ

Classification: OXIDOREDUCTASE

Total Structure Weight: 129191.87

Macromolecule Entities
Molecule Chains Length Organism Details
2-amino-5-chlorophenol 1,6-dioxygenase alpha subunit A, C 271 Comamonas testosteroni EC#: 1.13.11.8 IUBMB
Gene Name(s): cnbCa amnA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
2-amino-5-chlorophenol 1,6-dioxygenase beta subunit B, D 312 Comamonas testosteroni EC#: 1.13.11.74 IUBMB
Gene Name(s): cnbCb amnB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
2XP
Query on 2XP

B (2Z,4Z)-2-imino-6-oxohex-4-enoic acid
C6 H7 N O3
IZBQCPKKCVTOTK-PQZOIKATSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
2X7
Query on 2X7

D (3E)-3-iminooxepin-2(3H)-one
(4Z,6Z)-3-iminooxepin-2(3H)-one (Synonym)
C6 H5 N O2
HQPIXVSGYRVKOL-FNORWQNLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

B, D FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OH
Query on OH

D HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.190
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 270.24 α = 90.00
b = 48.39 β = 109.57
c = 108.55 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-25
  • Released Date: 2013-01-16
  • Deposition author(s): Li, D.F., Hou, Y.J., Hu, Y., Wang, D.C., Liu, W.

Revision History

No revisions since initial release