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

Crystal structure of the mimivirus NDK +Kpn mutant complexed with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-hexamer

Ligands

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

GDP.1: 12 residues within 4Å: Chain A: K.14, Y.55, H.58, Y.63, N.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.14, A:R.108, A:R.116, A:R.116, A:N.118 Water bridges: A:K.14, A:H.58, A:H.58, A:N.67, A:N.67, A:R.91, 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, A:Y.63 GDP.3: 12 residues within 4Å: Chain B: K.14, Y.55, H.58, Y.63, N.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.4 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:K.14, B:R.108, B:R.116, B:N.118 Water bridges: B:K.14, B:Y.55, B:Y.63, B:R.91, B:R.91, B:R.91, B:Q.94, B:T.97, B:R.116, B:R.116, B:R.116, B:R.116, B:H.121 Salt bridges: B:H.58, B:R.91, B:R.108 pi-Stacking: B:Y.63, B:Y.63 GDP.5: 12 residues within 4Å: Chain C: K.14, Y.55, H.58, Y.63, N.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.6 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:K.14, C:R.108, C:R.116, C:R.116, C:N.118 Water bridges: C:K.14, C:H.58, C:H.58, C:N.67, C:N.67, C:R.91, 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, C:Y.63 GDP.7: 12 residues within 4Å: Chain D: K.14, Y.55, H.58, Y.63, N.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.8 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:K.14, D:R.108, D:R.116, D:N.118 Water bridges: D:K.14, D:Y.55, D:Y.63, D:R.91, D:R.91, D:R.91, D:Q.94, D:T.97, D:R.116, D:R.116, D:R.116, D:R.116, D:H.121 Salt bridges: D:H.58, D:R.91, D:R.108 pi-Stacking: D:Y.63, D:Y.63 GDP.9: 12 residues within 4Å: Chain E: K.14, Y.55, H.58, Y.63, N.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.10 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:K.14, E:R.108, E:R.116, E:R.116, E:N.118 Water bridges: E:K.14, E:H.58, E:H.58, E:N.67, E:N.67, E:R.91, 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, E:Y.63 GDP.11: 12 residues within 4Å: Chain F: K.14, Y.55, H.58, Y.63, N.67, R.91, T.97, R.108, I.115, R.116, N.118 Ligands: MG.12 22 PLIP interactions: 22 interactions with chain F Hydrogen bonds: F:K.14, F:R.108, F:R.116, F:N.118 Water bridges: F:K.14, F:Y.55, F:Y.63, F:R.91, F:R.91, F:R.91, F:Q.94, F:T.97, F:R.116, F:R.116, F:R.116, F:R.116, F:H.121 Salt bridges: F:H.58, F:R.91, F:R.108 pi-Stacking: F:Y.63, F:Y.63

6 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: GDP.1 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: GDP.3 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: GDP.7 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: GDP.9 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: GDP.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

2009-08-25

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

Related Entries With Identical Sequence