› 4dz6

X-ray diffraction
2.2Å resolution

Transition state mimic of nucleoside-diphosphate kinase from borrelia burgdorferi with bound vanadate and adp

Released:
DOI: 10.2210/pdb4dz6/pdb
PDB entry 4dz6 coloured by chain, front view.
PDB entry 4dz6 coloured by chain, side view.
PDB entry 4dz6 coloured by chain, top view.
Source organism: Borreliella burgdorferi
Primary publication:
Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties.
Dumais M, Davies DR, Lin T, Staker BL, Myler PJ, Van Voorhis WC
Acta Crystallogr F Struct Biol Commun 74 373-384 (2018)
PMID: 29870023

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 hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129358 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 190 amino acids
Theoretical weight: 21.69 KDa
Source organism: Borreliella burgdorferi
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O51419 (Residues: 1-167; Coverage: 100%)
Gene names: BB_0463, ndk
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

4 bound ligands:
Ligand ADP 3 x ADP
Ligand VN4 3 x VN4
Ligand EDO 2 x EDO
Ligand VO4 3 x VO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P212121
Unit cell:
a: 78.65Å b: 81Å c: 181.43Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.183 0.223
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter.
Lacabanne et al. (2020)

1 mention without citation

Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties.
Dumais et al. (2018)