SMTL ID : 6xpv.1

Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to dTDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

TYD.1: 7 residues within 4Å: Chain A: K.20, L.63, F.68, L.72, R.96, T.102, V.120 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.68 Hydrogen bonds: A:K.20, A:T.102 Salt bridges: A:R.96 pi-Stacking: A:F.68 TYD.2: 7 residues within 4Å: Chain B: K.20, L.63, F.68, L.72, R.96, T.102, V.120 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:F.68, B:T.102 Hydrogen bonds: B:K.20, B:T.102 Water bridges: B:R.96, B:R.96, B:R.96, B:T.102, B:H.126, D:E.160, D:E.160, D:E.160 Salt bridges: B:R.96 pi-Stacking: B:F.68 TYD.3: 6 residues within 4Å: Chain C: L.63, F.68, L.72, R.96, T.102, V.120 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.68, C:T.102, C:V.120 Hydrogen bonds: C:T.102 Water bridges: C:R.96, C:R.96, C:H.126 Salt bridges: C:R.96 pi-Stacking: C:F.68 TYD.4: 7 residues within 4Å: Chain D: K.20, L.63, F.68, L.72, R.96, T.102, G.121 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.68, D:T.102 Hydrogen bonds: D:K.20, D:T.102 Water bridges: D:K.20, D:R.96, D:R.96, D:R.96, D:N.123 Salt bridges: D:R.96 pi-Stacking: D:F.68 TYD.5: 8 residues within 4Å: Chain E: K.20, Y.60, L.63, F.68, L.72, R.96, T.102, V.120 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:F.68, E:T.102, E:V.120 Hydrogen bonds: E:K.20, E:Y.60, E:T.102 Water bridges: E:R.96, E:H.126, E:D.129, A:E.160 Salt bridges: E:R.96 pi-Stacking: E:F.68 TYD.6: 6 residues within 4Å: Chain F: L.63, F.68, L.72, R.96, T.102, V.120 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:F.68, F:T.102, F:V.120 Hydrogen bonds: F:T.102 Water bridges: F:K.20, F:K.20, F:R.96, F:R.96, E:E.160 Salt bridges: F:R.96 pi-Stacking: F:F.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, S. et al., Nucleoside selectivity of Aspergillus fumigatus nucleoside-diphosphate kinase. Febs J. (2021)

Release Date

2020-11-04

Peptides

Nucleoside diphosphate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
G

F
H

Nucleoside diphosphate kinase

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