› 3zpc

X-ray diffraction
2.2Å resolution

Acinetobacter baumannii RibD, form 1

Released:
DOI: 10.2210/pdb3zpc/pdb
PDB entry 3zpc coloured by chain, front view.
PDB entry 3zpc coloured by chain, side view.
PDB entry 3zpc coloured by chain, top view.
Source organism: Acinetobacter baumannii
Primary publication:
Structure of diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase from Acinetobacter baumannii.
Dawson A, Trumper P, Chrysostomou G, Hunter WN
Acta Crystallogr Sect F Struct Biol Cryst Commun 69 611-7 (2013)
PMID: 23722836

Function and Biology Details

Reactions catalysed: 
5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H(2)O = 5-amino-6-(5-phosphoribosylamino)uracil + NH(3)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111938 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Riboflavin biosynthesis protein RibD Chains: A, B
Molecule details ›
Chains: A, B
Length: 382 amino acids
Theoretical weight: 42.09 KDa
Source organism: Acinetobacter baumannii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D0CB74 (Residues: 1-361; Coverage: 100%)
Gene names: HMPREF0010_02004, ribD
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand ACT 1 x ACT
Ligand PO4 4 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2221
Unit cell:
a: 148.987Å b: 189.555Å c: 76.406Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.213 0.25
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Inhibitors of riboflavin biosynthetic pathway enzymes as potential antibacterial drugs.
Islam et al. (2023)

1 mention without citation

Structure of diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase from Acinetobacter baumannii.
Dawson et al. (2013)