› 5yih

X-ray diffraction
1.98Å resolution

Crystal structure of tetrameric Nucleoside diphosphate kinase at 1.98 A resolution from Acinetobacter baumannii

Released:
DOI: 10.2210/pdb5yih/pdb
Model geometry
Fit model/data
PDB entry 5yih coloured by chain, front view.
PDB entry 5yih coloured by chain, side view.
PDB entry 5yih coloured by chain, top view.
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Entry authors: Bairagya HR, Sikarwar J, Iqbal N, Singh PK, Kaur P, Sharma S, Singh TP

Function and Biology Details

Reaction catalysed: 
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111935 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 143 amino acids
Theoretical weight: 15.48 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Expression system: Escherichia coli
UniProt:
  • Canonical: D0CAF1 (Residues: 1-143; Coverage: 100%)
Gene names: HMPREF0010_01731, ndk
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

1 bound ligand:
Ligand MG 5 x MG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: C2
Unit cell:
a: 145.88Å b: 70.47Å c: 68.85Å
α: 90° β: 109.4° γ: 90°
R-values:
R R work R free
0.205 0.202 0.256
Expression system: Escherichia coli

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