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

Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 8 residues within 4Å: Chain A: H.58, Y.63, L.67, R.91, Q.94, G.95, R.104, I.111 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.58, A:Q.94, A:G.112 Salt bridges: A:R.91, A:R.91, A:R.104, A:R.104 GDP.3: 11 residues within 4Å: Chain B: K.14, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, G.112, N.114 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.14, B:Q.94, B:Q.94, B:R.104, B:N.114, B:N.114 Salt bridges: B:H.58, B:R.91, B:R.104 pi-Stacking: B:Y.63, B:Y.63 GDP.5: 12 residues within 4Å: Chain C: K.14, Y.55, H.58, L.67, R.91, Q.94, R.104, I.111, G.112, N.114, H.117 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.14, C:Q.94, C:R.104, C:N.114, C:N.114, C:H.117 Salt bridges: C:H.58, C:R.91, C:R.104 pi-Stacking: C:Y.63, C:Y.63 GDP.6: 8 residues within 4Å: Chain D: H.58, Y.63, L.67, R.91, Q.94, G.95, R.104, I.111 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:H.58, D:Q.94, D:G.112 Salt bridges: D:R.91, D:R.91, D:R.104, D:R.104 GDP.8: 11 residues within 4Å: Chain E: K.14, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, G.112, N.114 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:K.14, E:Q.94, E:Q.94, E:R.104, E:N.114, E:N.114 Salt bridges: E:H.58, E:R.91, E:R.104 pi-Stacking: E:Y.63, E:Y.63 GDP.10: 12 residues within 4Å: Chain F: K.14, Y.55, H.58, L.67, R.91, Q.94, R.104, I.111, G.112, N.114, H.117 Ligands: MG.9 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:K.14, F:Q.94, F:R.104, F:N.114, F:N.114 Salt bridges: F:H.58, F:R.91, F:R.104 pi-Stacking: F:Y.63, F:Y.63

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: K.14, Y.55, R.104, H.117 Ligands: GDP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Y.55, B:H.117 MG.4: 3 residues within 4Å: Chain C: R.91, D.120 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain E: K.14, Y.55, R.104, H.117 Ligands: GDP.8 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:Y.55, E:H.117 MG.9: 3 residues within 4Å: Chain F: R.91, D.120 Ligands: GDP.10 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

2009-06-16

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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