SMTL ID : 2b8p.1

Crystal structure of Acanthamoeba polyphaga mimivirus NDK, the first viral nucleoside diphosphate kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-hexamer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: K.29, Y.70, R.106, R.119, N.129, H.132 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.106, A:N.129 Salt bridges: A:K.29, A:R.119, A:H.132 SO4.2: 5 residues within 4Å: Chain A: G.110, N.111, I.112, R.119, I.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.112 Salt bridges: A:R.119 SO4.3: 6 residues within 4Å: Chain B: K.29, Y.70, R.106, R.119, N.129, H.132 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.106, B:N.129 Water bridges: B:K.29, B:K.29 Salt bridges: B:K.29, B:R.119, B:H.132 SO4.4: 3 residues within 4Å: Chain B: H.73, Q.76, Y.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.76, B:Y.78 SO4.5: 6 residues within 4Å: Chain C: K.29, Y.70, R.106, R.119, N.129, H.132 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.70, C:R.106, C:N.129 Salt bridges: C:K.29, C:R.119, C:H.132 SO4.6: 5 residues within 4Å: Chain C: G.110, N.111, I.112, R.119, I.126 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.112 Salt bridges: C:R.119 SO4.7: 6 residues within 4Å: Chain D: K.29, Y.70, R.106, R.119, N.129, H.132 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.106, D:N.129 Water bridges: D:K.29, D:K.29 Salt bridges: D:K.29, D:R.119, D:H.132 SO4.8: 3 residues within 4Å: Chain D: H.73, Q.76, Y.78 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.76, D:Y.78 SO4.9: 6 residues within 4Å: Chain E: K.29, Y.70, R.106, R.119, N.129, H.132 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Y.70, E:R.106, E:N.129 Salt bridges: E:K.29, E:R.119, E:H.132 SO4.10: 5 residues within 4Å: Chain E: G.110, N.111, I.112, R.119, I.126 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.112 Salt bridges: E:R.119 SO4.11: 6 residues within 4Å: Chain F: K.29, Y.70, R.106, R.119, N.129, H.132 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:R.106, F:N.129 Water bridges: F:K.29, F:K.29 Salt bridges: F:K.29, F:R.119, F:H.132 SO4.12: 3 residues within 4Å: Chain F: H.73, Q.76, Y.78 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.76, F:Y.78

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

2005-11-15

Peptides

Probable nucleoside diphosphate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Probable nucleoside diphosphate kinase

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