SMTL ID : 3g2x.2 (1 other biounit)

Structure of mimivirus NDK +Kpn - N62L double mutant complexed with dTDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: H.58, H.121 Ligands: TYD.2 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Ligands: TYD.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: R.91, D.124 Ligands: TYD.6 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain D: H.58, H.121 Ligands: TYD.8 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: TYD.10 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain F: R.91, D.124 Ligands: TYD.12 No protein-ligand interaction detected (PLIP)

6 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.2: 12 residues within 4Å: Chain A: K.14, Y.55, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.108, A:R.116, A:N.118 Salt bridges: A:H.58, A:R.91, A:R.108 pi-Stacking: A:Y.63 TYD.4: 12 residues within 4Å: Chain B: K.14, Y.55, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.63 Hydrogen bonds: B:K.14, B:Y.63, B:T.97, B:R.116, B:N.118 Water bridges: B:R.91, B:R.91 Salt bridges: B:H.58, B:R.91, B:R.108 pi-Stacking: B:Y.63 TYD.6: 11 residues within 4Å: Chain C: K.14, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.63 Hydrogen bonds: C:K.14, C:R.108, C:N.118 Salt bridges: C:H.58, C:R.91, C:R.108 pi-Stacking: C:Y.63 TYD.8: 12 residues within 4Å: Chain D: K.14, Y.55, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.7 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.97, D:R.108, D:R.116, D:N.118 Salt bridges: D:H.58, D:R.91, D:R.108 pi-Stacking: D:Y.63 TYD.10: 12 residues within 4Å: Chain E: K.14, Y.55, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.9 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:Y.63 Hydrogen bonds: E:K.14, E:Y.55, E:R.116, E:N.118 Water bridges: E:R.91, E:R.91 Salt bridges: E:H.58, E:R.91, E:R.108 pi-Stacking: E:Y.63 TYD.12: 11 residues within 4Å: Chain F: K.14, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.11 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:Y.63 Hydrogen bonds: F:K.14, F:T.97, F:R.108, F:N.118 Salt bridges: F:H.58, F:R.91, F:R.108 pi-Stacking: F:Y.63

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
D

B
E

C
F

D
D

E
E

F
F

Nucleoside diphosphate kinase

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