› 5v6d

X-ray diffraction
1.85Å resolution

Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate

Released:
DOI: 10.2210/pdb5v6d/pdb
PDB entry 5v6d coloured by chain, front view.
PDB entry 5v6d coloured by chain, side view.
PDB entry 5v6d coloured by chain, top view.
Source organism: Neisseria gonorrhoeae NCCP11945
Entry author: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110118 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Length: 149 amino acids
Theoretical weight: 16.49 KDa
Source organism: Neisseria gonorrhoeae NCCP11945
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B4RMG0 (Residues: 1-141; Coverage: 100%)
Gene names: NGK_1320, ndk
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

2 bound ligands:
Ligand CIT 16 x CIT
Ligand EDO 22 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P1
Unit cell:
a: 57.24Å b: 112.35Å c: 112.87Å
α: 104.31° β: 98.5° γ: 105.39°
R-values:
R R work R free
0.15 0.15 0.188
Expression system: Escherichia coli BL21(DE3)

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