› 1wkl

X-ray diffraction
2.2Å resolution

Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with ATP and ADP

Released:
DOI: 10.2210/pdb1wkl/pdb
PDB entry 1wkl coloured by chain, front view.
PDB entry 1wkl coloured by chain, side view.
PDB entry 1wkl coloured by chain, top view.
Source organism: Thermus thermophilus
Entry authors: Takeishi S, Nakagawa N, Masui R, Kuramitsu S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo hexamer (preferred)
homo dodecamer
Assembly name:
PDBe Complex ID:
PDB-CPX-178218 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 137 amino acids
Theoretical weight: 15.37 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SLV5 (Residues: 1-137; Coverage: 100%)
Gene names: TTHA0188, ndk
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

4 bound ligands:
Ligand PHS 1 x PHS
Ligand ADP 1 x ADP
Ligand MG 1 x MG
Ligand ATP 1 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P6322
Unit cell:
a: 122.897Å b: 122.897Å c: 105.492Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.217 0.217 0.237
Expression system: Escherichia coli BL21(DE3)

Quick links