SMTL ID : 1s59.1

Structure of nucleoside diphosphate kinase 2 with bound dGTP from Arabidopsis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

1 x DGI: 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE(Non-covalent)

DGI.1: 11 residues within 4Å: Chain A: L.56, F.61, L.65, R.89, T.95, R.106, T.113, G.114, N.116, G.120 Chain C: E.153 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.13, A:T.95, A:N.116 Water bridges: A:R.89, A:R.89 Salt bridges: A:R.89, A:R.106, C:E.153 pi-Stacking: A:F.61, A:F.61

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.2: 14 residues within 4Å: Chain B: E.153 Chain C: K.13, Y.53, L.56, F.61, L.65, T.95, R.106, T.113, G.114, N.116, V.118, H.119, G.120 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Y.53, C:Y.53, C:Y.53, C:T.95, C:R.106, C:N.116, C:H.119, C:G.120 Water bridges: C:G.114, B:E.153 Salt bridges: C:K.13, C:R.106, C:R.106, C:H.119, B:E.153 pi-Stacking: C:F.61, C:F.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Im, Y.J. et al., Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling. J.Mol.Biol. (2004)

Release Date

2004-11-30

Peptides

Nucleoside diphosphate kinase II: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleoside diphosphate kinase II

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