SMTL ID : 3fc9.2 (1 other biounit)

Crystal structure of the Mimivirus NDK +Kpn-N62L double mutant complexed with CDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

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

6 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.2: 13 residues within 4Å: Chain A: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, T.97, R.108, I.115, R.116, N.118 Ligands: MG.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.115 Hydrogen bonds: A:K.14, A:Q.94, A:T.97, A:R.108, A:R.116, A:N.118, A:N.118 Water bridges: A:K.14, A:Y.55 Salt bridges: A:H.58, A:R.91, A:R.108 pi-Stacking: A:Y.63 CDP.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 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.115 Hydrogen bonds: B:K.14, B:R.108, B:R.116, B:N.118, B:N.118 Salt bridges: B:H.58, B:R.91, B:R.108 pi-Stacking: B:Y.63 CDP.6: 13 residues within 4Å: Chain C: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, T.97, R.108, I.115, R.116, N.118 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.115 Hydrogen bonds: C:K.14, C:Q.94, C:T.97, C:T.97, C:R.108, C:R.116, C:N.118, C:N.118 Salt bridges: C:H.58, C:R.91, C:R.108 pi-Stacking: C:Y.63 CDP.8: 13 residues within 4Å: Chain D: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, T.97, R.108, I.115, R.116, N.118 Ligands: MG.7 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.115 Hydrogen bonds: D:K.14, D:Q.94, D:R.108, D:R.116, D:N.118, D:N.118 Water bridges: D:Y.55, D:H.121 Salt bridges: D:H.58, D:R.91, D:R.108 pi-Stacking: D:Y.63 CDP.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:I.115 Hydrogen bonds: E:K.14, E:T.97, E:R.108, E:R.116, E:N.118, E:N.118 Salt bridges: E:H.58, E:R.91, E:R.108 pi-Stacking: E:Y.63 CDP.12: 13 residues within 4Å: Chain F: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, T.97, R.108, I.115, R.116, N.118 Ligands: MG.11 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:I.115 Hydrogen bonds: F:K.14, F:Q.94, F:T.97, F:R.108, F:R.116, F:N.118, 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

2009-08-25

Peptides

Nucleoside diphosphate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
C

E
D

F
E

Nucleoside diphosphate kinase

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