2NW8

Crystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris in complex with ferrous heme and tryptophan. Northeast Structural Genomics Target XcR13.

Structural Biology Knowledgebase: 2NW8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.171

Literature

Macromolecules
Sequence Display for 2NW8

Classification: OXIDOREDUCTASE

Total Structure Weight: 73214.90

Macromolecule Entities
Molecule Chains Length Organism Details
Tryptophan 2,3-dioxygenase A, B 306 Xanthomonas campestris EC#: 1.13.11.11 IUBMB
Gene Name(s): kynA XCC0432
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRP
Query on TRP

A, B TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.171
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 114.09 α = 90.00
b = 114.09 β = 90.00
c = 96.23 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-11-14
  • Released Date: 2006-12-19
  • Deposition author(s): Forouhar, F., Anderson, J.L.R., Mowat, C.G., Bruckmann, C., Thackray, S.J., Seetharaman, J., Ho, C.K., Ma, L.C., Cunningham, K., Janjua, H., Zhao, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Champman, S.K., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values