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

Crystal structure of the mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with TDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: D.124 Ligands: TYD.2 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Ligands: TYD.4 No protein-ligand interaction detected (PLIP)

2 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.2: 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.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.63 Hydrogen bonds: A:K.14, A:T.97, A:R.108, A:N.118 Water bridges: A:K.14, A:Y.55, A:Q.94, A:Q.94, A:T.97 Salt bridges: A:H.58, A:R.91, A:R.108 pi-Stacking: A:Y.63 TYD.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, G.116, N.118 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.63 Hydrogen bonds: B:K.14, B:T.97, B:R.108, B:N.118 Water bridges: B:K.14, B:Y.55, B:Q.94, B:Q.94, B:H.121, B:D.124 Salt bridges: B:H.58, B:R.91, B:R.108 pi-Stacking: B: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

2009-06-16

Peptides

Nucleoside diphosphate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nucleoside diphosphate kinase

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