› 2f67

X-ray diffraction
1.6Å resolution

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

Released:
DOI: 10.2210/pdb2f67/pdb
PDB entry 2f67 coloured by chain, front view.
PDB entry 2f67 coloured by chain, side view.
PDB entry 2f67 coloured by chain, top view.
Source organism: Trypanosoma brucei
Primary publication:
Using fragment cocktail crystallography to assist inhibitor design of Trypanosoma brucei nucleoside 2-deoxyribosyltransferase.
Bosch J, Robien MA, Mehlin C, Boni E, Riechers A, Buckner FS, Van Voorhis WC, Myler PJ, Worthey EA, DeTitta G, Luft JR, Lauricella A, Gulde S, Anderson LA, Kalyuzhniy O, Neely HM, Ross J, Earnest TN, Soltis M, Schoenfeld L, Zucker F, Merritt EA, Fan E, Verlinde CL, Hol WG
J Med Chem 49 5939-46 (2006)
PMID: 17004709

Function and Biology Details

Reaction catalysed: 
2-deoxy-D-ribosyl-base(1) + base(2) = 2-deoxy-D-ribosyl-base(2) + base(1)
Biochemical function:
Biological process:
Cellular component:
Sequence domain:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176531 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside 2-deoxyribosyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 161 amino acids
Theoretical weight: 18.66 KDa
Source organism: Trypanosoma brucei
Expression system: Escherichia coli
UniProt:
  • Canonical: Q57VC7 (Residues: 1-153; Coverage: 100%)
Gene names: Tb05.30H13.400, Tb927.5.1360
Sequence domains: Nucleoside 2-deoxyribosyltransferase
Structure domains: Rossmann fold

Ligands and Environments

3 bound ligands:
Ligand SO4 3 x SO4
Ligand 12B 2 x 12B
Ligand GOL 2 x GOL
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: C2
Unit cell:
a: 58.928Å b: 75.513Å c: 86.336Å
α: 90° β: 90.01° γ: 90°
R-values:
R R work R free
0.179 0.178 0.208
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Structural biology in fragment-based drug design.
Murray et al. (2010)
8 more

3 mentions without citation

Fragment-based cocktail crystallography by the medical structural genomics of pathogenic protozoa consortium.
Verlinde et al. (2009)
2 more