SMTL ID : 3fcv.1

Crystal structure of the Mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with dUDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x DUD: DEOXYURIDINE-5'-DIPHOSPHATE(Non-covalent)

DUD.1: 12 residues within 4Å: Chain A: K.14, Y.55, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, G.116, N.118 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.97 Hydrogen bonds: A:K.14, A:T.97, A:R.108, A:N.118, A:N.118 Water bridges: A:Q.94, A:Q.94, A:T.97, A:H.121 Salt bridges: A:H.58, A:R.91, A:R.108 pi-Stacking: A:Y.63 DUD.3: 12 residues within 4Å: Chain B: K.14, Y.55, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, G.116, N.118 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:K.14, B:Y.55, B:T.97, B:R.108, B:N.118, B:N.118 Water bridges: B:R.91, B:R.91, B:R.91, B:Q.94, B:H.121 Salt bridges: B:H.58, B:R.91, B:R.108 pi-Stacking: B:Y.63 DUD.5: 12 residues within 4Å: Chain C: K.14, Y.55, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, G.116, N.118 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:T.97 Hydrogen bonds: C:K.14, C:T.97, C:R.108, C:N.118, C:N.118 Water bridges: C:Q.94, C:Q.94, C:T.97, C:H.121 Salt bridges: C:H.58, C:R.91, C:R.108 pi-Stacking: C:Y.63 DUD.7: 12 residues within 4Å: Chain D: K.14, Y.55, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, G.116, N.118 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:K.14, D:Y.55, D:T.97, D:R.108, D:N.118, D:N.118 Water bridges: D:R.91, D:R.91, D:R.91, D:Q.94, D:H.121 Salt bridges: D:H.58, D:R.91, D:R.108 pi-Stacking: D:Y.63 DUD.9: 12 residues within 4Å: Chain E: K.14, Y.55, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, G.116, N.118 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:T.97 Hydrogen bonds: E:K.14, E:T.97, E:R.108, E:N.118, E:N.118 Water bridges: E:Q.94, E:Q.94, E:T.97, E:H.121 Salt bridges: E:H.58, E:R.91, E:R.108 pi-Stacking: E:Y.63 DUD.11: 12 residues within 4Å: Chain F: K.14, Y.55, H.58, Y.63, L.67, R.91, T.97, R.108, I.115, G.116, N.118 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:K.14, F:Y.55, F:T.97, F:R.108, F:N.118, F:N.118 Water bridges: F:R.91, F:R.91, F:R.91, F:Q.94, F:H.121 Salt bridges: F:H.58, F:R.91, F:R.108 pi-Stacking: F:Y.63

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.124 Ligands: DUD.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.124, H2O.2, H2O.3 MG.4: 3 residues within 4Å: Chain B: Y.55, H.58 Ligands: DUD.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: D.124 Ligands: DUD.5 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.124, H2O.7, H2O.7 MG.8: 3 residues within 4Å: Chain D: Y.55, H.58 Ligands: DUD.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain E: D.124 Ligands: DUD.9 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.124, H2O.11, H2O.11 MG.12: 3 residues within 4Å: Chain F: Y.55, H.58 Ligands: DUD.11 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
A

D
B

E
A

F
B

Nucleoside diphosphate kinase

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