› 8qw3

X-ray diffraction
1.26Å resolution

Human NDPK-C in complex with ADP

Released:
DOI: 10.2210/pdb8qw3/pdb
Model geometry
Fit model/data
PDB entry 8qw3 coloured by chain, front view.
PDB entry 8qw3 coloured by chain, side view.
PDB entry 8qw3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes.
Amjadi R, Werten S, Lomada SK, Baldin C, Scheffzek K, Dunzendorfer-Matt T, Wieland T
Int J Mol Sci 25 (2024)
PMID: 39337255

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171611 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase 3 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 155 amino acids
Theoretical weight: 17.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13232 (Residues: 18-169; Coverage: 90%)
Gene name: NME3
Sequence domains: Nucleoside diphosphate kinase

Ligands and Environments

2 bound ligands:
Ligand ADP 6 x ADP
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P1
Unit cell:
a: 52.315Å b: 67.865Å c: 68.423Å
α: 108.492° β: 112.343° γ: 101.105°
R-values:
R R work R free
0.147 0.147 0.176
Expression system: Escherichia coli

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