2F67

Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6 A resolution with BENZO[CD]INDOL-2(1H)-ONE bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 2F67

Classification: TRANSFERASE

Total Structure Weight: 38138.87

Macromolecule Entities
Molecule Chains Length Organism Details
Nucleoside 2-deoxyribosyltransferase A, B 161 Trypanosoma brucei EC#: 2.4.2.6 IUBMB
Mutation: M9M, M24M, M42M, G53E, M64M, Y93C, M100M, M111M, E118G, M136M
Gene Name(s): Tb927.5.1360
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
12B
Query on 12B

A, B BENZO[CD]INDOL-2(1H)-ONE
C11 H7 N O
GPYLCFQEKPUWLD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.178
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 58.93 α = 90.00
b = 75.51 β = 90.01
c = 86.34 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-28
  • Released Date: 2005-12-06
  • Deposition author(s): Bosch, J., Robien, M.A., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History

  • Version 1_0: 2005-12-06

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Advisory, Version format compliance