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

Crystal structure of the Mimivirus NDK N62L mutant complexed with CDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

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

CDP.1: 12 residues within 4Å: Chain A: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, R.112, N.114 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.14, A:Q.94, A:R.104, A:R.112, A:N.114, A:N.114 Water bridges: A:K.14, A:R.91 Salt bridges: A:H.58, A:R.91, A:R.104 pi-Stacking: A:Y.63 CDP.3: 12 residues within 4Å: Chain B: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, R.112, N.114 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.111 Hydrogen bonds: B:K.14, B:R.104, B:R.112, B:N.114, B:N.114 Water bridges: B:K.14 Salt bridges: B:H.58, B:R.91, B:R.104 pi-Stacking: B:Y.63 CDP.5: 11 residues within 4Å: Chain C: K.14, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, R.112, N.114 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:K.14, C:Q.94, C:R.104, C:R.112, C:N.114, C:N.114 Water bridges: C:K.14, C:R.91, C:R.91, C:H.117 Salt bridges: C:H.58, C:R.91, C:R.104 pi-Stacking: C:Y.63 CDP.7: 12 residues within 4Å: Chain D: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, R.112, N.114 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:K.14, D:Q.94, D:R.104, D:R.112, D:N.114, D:N.114 Water bridges: D:K.14, D:Y.55, D:R.91 Salt bridges: D:H.58, D:R.91, D:R.104 pi-Stacking: D:Y.63 CDP.9: 12 residues within 4Å: Chain E: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, R.112, N.114 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:I.111 Hydrogen bonds: E:K.14, E:R.104, E:R.112, E:N.114, E:N.114 Water bridges: E:K.14, E:Y.55 Salt bridges: E:H.58, E:R.91, E:R.104 pi-Stacking: E:Y.63 CDP.11: 11 residues within 4Å: Chain F: K.14, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, R.112, N.114 Ligands: MG.12 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:K.14, F:Q.94, F:R.104, F:R.112, F:N.114, F:N.114 Water bridges: F:K.14, F:Y.55, F:R.91, F:R.91 Salt bridges: F:H.58, F:R.91, F:R.104 pi-Stacking: F:Y.63

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: R.91, D.120 Ligands: CDP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: R.91 Ligands: CDP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: R.91, D.120 Ligands: CDP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: R.91, D.120 Ligands: CDP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain E: R.91 Ligands: CDP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain F: R.91, D.120 Ligands: CDP.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
B

B
D

C
F

D
B

E
D

F
F

Nucleoside diphosphate kinase

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