› › Structure analysis

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

X-ray diffraction
1.85Å resolution
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
Assembly composition:
homo dimer (preferred)
Entry contents: 1 distinct polypeptide molecule

Quick links

Assemblies

Assembly 1
Download    3D Visualisation
Assembly Name: Nucleoside diphosphate kinase
hide full assembly name
Multimeric state: homo dimer
Accessible surface area: 12319.4 Å2
Buried surface area: 3151.58 Å2
Dissociation area: 926.03 Å2
Dissociation energy (ΔGdiss): 9.79 kcal/mol
Dissociation entropy (TΔSdiss): 11.74 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-110118
Assembly 2
Download    3D Visualisation
Assembly Name: Nucleoside diphosphate kinase
hide full assembly name
Multimeric state: homo dimer
Accessible surface area: 12204.11 Å2
Buried surface area: 3261.63 Å2
Dissociation area: 944.38 Å2
Dissociation energy (ΔGdiss): 9.19 kcal/mol
Dissociation entropy (TΔSdiss): 11.74 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-110118
Assembly 3 (preferred)
Download    3D Visualisation
Assembly Name: Nucleoside diphosphate kinase
hide full assembly name
Multimeric state: homo dimer
Accessible surface area: 12322.74 Å2
Buried surface area: 3067.59 Å2
Dissociation area: 913.18 Å2
Dissociation energy (ΔGdiss): 11.32 kcal/mol
Dissociation entropy (TΔSdiss): 11.74 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-110118
Assembly 4
Download    3D Visualisation
Assembly Name: Nucleoside diphosphate kinase
hide full assembly name
Multimeric state: homo dimer
Accessible surface area: 12457.2 Å2
Buried surface area: 3494.89 Å2
Dissociation area: 1,015.61 Å2
Dissociation energy (ΔGdiss): 5.7 kcal/mol
Dissociation entropy (TΔSdiss): 11.8 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-110118
Assembly 5
Download    3D Visualisation
Assembly Name: Nucleoside diphosphate kinase
hide full assembly name
Multimeric state: homo dimer
Accessible surface area: 12440.07 Å2
Buried surface area: 3073.38 Å2
Dissociation area: 925 Å2
Dissociation energy (ΔGdiss): 10.15 kcal/mol
Dissociation entropy (TΔSdiss): 11.76 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-110118
Assembly 6
Download    3D Visualisation
Assembly Name: Nucleoside diphosphate kinase
hide full assembly name
Multimeric state: homo dimer
Accessible surface area: 12382.25 Å2
Buried surface area: 3287.52 Å2
Dissociation area: 999.63 Å2
Dissociation energy (ΔGdiss): 7.46 kcal/mol
Dissociation entropy (TΔSdiss): 11.78 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-110118
Assembly 7
Download    3D Visualisation
Assembly Name: Nucleoside diphosphate kinase
hide full assembly name
Multimeric state: homo dimer
Accessible surface area: 12451.37 Å2
Buried surface area: 3217.2 Å2
Dissociation area: 955.37 Å2
Dissociation energy (ΔGdiss): 8.81 kcal/mol
Dissociation entropy (TΔSdiss): 11.78 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-110118
Assembly 8
Download    3D Visualisation
Assembly Name: Nucleoside diphosphate kinase
hide full assembly name
Multimeric state: homo dimer
Accessible surface area: 12190.45 Å2
Buried surface area: 2998.48 Å2
Dissociation area: 881.79 Å2
Dissociation energy (ΔGdiss): 10.15 kcal/mol
Dissociation entropy (TΔSdiss): 11.72 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-110118

Macromolecules

Nucleoside diphosphate kinase
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
Pfam: Nucleoside diphosphate kinase
InterPro:
CATH: Nucleoside diphosphate kinase-like domain
Nucleoside diphosphate kinase in PDB entry 5v6d, assembly 3, front view.
Nucleoside diphosphate kinase in PDB entry 5v6d, assembly 3, side view.
Nucleoside diphosphate kinase in PDB entry 5v6d, assembly 3, top view.
Molecule details ›

Search similar proteins

Quick links