SMTL ID : 3gp9.2 (1 other biounit)

Crystal structure of the Mimivirus NDK complexed with GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 14 residues within 4Å: Chain A: K.14, Y.55, H.58, Y.63, N.67, R.91, Q.94, R.104, I.111, R.112, N.114, H.117 Ligands: PO4.2, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.94, A:R.112, A:N.114 Water bridges: A:K.14 Salt bridges: A:K.14, A:R.91, A:R.104, A:R.104, A:H.117 pi-Stacking: A:Y.63, A:Y.63 GDP.4: 12 residues within 4Å: Chain B: K.14, Y.55, H.58, Y.63, N.67, Q.94, R.104, I.111, R.112, N.114, H.117 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:K.14, B:K.14, B:Y.55, B:Y.55, B:Q.94, B:I.111, B:N.114 Water bridges: B:N.67, B:R.104 Salt bridges: B:K.14, B:R.91, B:R.104, B:R.104, B:H.117 pi-Stacking: B:Y.63 GDP.7: 12 residues within 4Å: Chain C: K.14, Y.55, H.58, Y.63, R.91, Q.94, R.104, I.111, R.112, N.114, H.117 Ligands: MG.9 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:H.58, C:Y.63, C:Q.94, C:N.114 Water bridges: C:K.14, C:R.91, C:R.112 Salt bridges: C:K.14, C:R.91, C:R.104, C:R.104, C:H.117 pi-Stacking: C:Y.63, C:Y.63 GDP.10: 14 residues within 4Å: Chain D: K.14, Y.55, H.58, Y.63, N.67, R.91, Q.94, R.104, I.111, R.112, N.114, H.117 Ligands: PO4.11, MG.12 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Y.55, D:Q.94, D:R.112, D:N.114 Water bridges: D:K.14 Salt bridges: D:K.14, D:R.91, D:R.104, D:R.104, D:H.117 pi-Stacking: D:Y.63, D:Y.63 GDP.13: 12 residues within 4Å: Chain E: K.14, Y.55, H.58, Y.63, N.67, Q.94, R.104, I.111, R.112, N.114, H.117 Ligands: MG.15 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:K.14, E:K.14, E:Y.55, E:Y.55, E:Y.55, E:Q.94, E:I.111, E:N.114 Water bridges: E:N.67, E:R.104 Salt bridges: E:K.14, E:R.91, E:R.104, E:R.104, E:H.117 pi-Stacking: E:Y.63 GDP.16: 12 residues within 4Å: Chain F: K.14, Y.55, H.58, Y.63, R.91, Q.94, R.104, I.111, R.112, N.114, H.117 Ligands: MG.18 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Y.55, F:H.58, F:Q.94, F:N.114 Water bridges: F:K.14, F:R.91, F:R.112 Salt bridges: F:K.14, F:R.91, F:R.104, F:R.104, F:H.117 pi-Stacking: F:Y.63, F:Y.63

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: N.96, I.97, R.104, D.110, I.111, N.114 Ligands: GDP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.97, A:N.114 Salt bridges: A:R.104 PO4.5: 6 residues within 4Å: Chain B: G.95, N.96, I.97, R.104, I.111, N.114 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.97, B:N.114 Water bridges: B:R.104 Salt bridges: B:R.104 PO4.8: 6 residues within 4Å: Chain C: G.95, N.96, I.97, R.104, D.110, N.114 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.95, C:I.97, C:N.114 Water bridges: C:Q.94 Salt bridges: C:R.104 PO4.11: 7 residues within 4Å: Chain D: N.96, I.97, R.104, D.110, I.111, N.114 Ligands: GDP.10 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.97, D:N.114 Salt bridges: D:R.104 PO4.14: 6 residues within 4Å: Chain E: G.95, N.96, I.97, R.104, I.111, N.114 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:I.97, E:N.114 Water bridges: E:R.104 Salt bridges: E:R.104 PO4.17: 6 residues within 4Å: Chain F: G.95, N.96, I.97, R.104, D.110, N.114 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.95, F:I.97, F:N.114 Water bridges: F:Q.94 Salt bridges: F:R.104

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: R.91, Q.94, R.104, H.117, A.118 Ligands: GDP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.117 MG.6: 5 residues within 4Å: Chain B: Q.94, R.104, H.117, A.118 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.9: 6 residues within 4Å: Chain C: R.91, Q.94, R.104, H.117, A.118 Ligands: GDP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.117 MG.12: 6 residues within 4Å: Chain D: R.91, Q.94, R.104, H.117, A.118 Ligands: GDP.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.117 MG.15: 5 residues within 4Å: Chain E: Q.94, R.104, H.117, A.118 Ligands: GDP.13 No protein-ligand interaction detected (PLIP) MG.18: 6 residues within 4Å: Chain F: R.91, Q.94, R.104, H.117, A.118 Ligands: GDP.16 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeudy, S. et al., Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase. J.Virol. (2009)

Release Date

2009-08-11

Peptides

Nucleoside diphosphate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
F

D
B

E
D

F
F

Nucleoside diphosphate kinase

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