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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 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

2 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)

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nucleoside diphosphate kinase

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