1s2d

X-ray diffraction
2.1Å resolution

Purine 2'-Deoxyribosyl complex with arabinoside: Ribosylated Intermediate (AraA)

Released:

Function and Biology Details

Reaction catalysed:
2-deoxy-D-ribosyl-base(1) + base(2) = 2-deoxy-D-ribosyl-base(2) + base(1) 
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
PDBe Complex ID:
PDB-CPX-186003 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside 2-deoxyribosyltransferase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 167 amino acids
Theoretical weight: 18.73 KDa
Source organism: Lactobacillus helveticus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8RLY5 (Residues: 1-167; Coverage: 100%)
Gene names: BC335_1936, GDZ32_10450, IMAU30003_01598, LH5_01102, LHEJCM1062_04650, ndtA, ntd_1, ptd
Sequence domains: Nucleoside 2-deoxyribosyltransferase
Structure domains: Rossmann fold

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 8-BM
Spacegroup: P43212
Unit cell:
a: 79.587Å b: 79.587Å c: 184.973Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.229 0.253
Expression system: Escherichia coli