SMTL ID : 6xpu.1

Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to IDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: IDP.2 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain B: D.62 Ligands: IDP.4 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: IDP.6 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: IDP.8 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain E: D.62 Ligands: IDP.10 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: IDP.12 No protein-ligand interaction detected (PLIP)

6 x IDP: INOSINE-5'-DIPHOSPHATE(Non-covalent)

IDP.2: 12 residues within 4Å: Chain A: K.20, Y.60, L.63, F.68, L.72, R.96, T.102, V.120, G.121, N.123 Chain F: E.160 Ligands: MG.1 18 PLIP interactions: 2 interactions with chain F, 16 interactions with chain A Water bridges: F:E.160, F:E.160, A:Y.60, A:R.96, A:R.96, A:R.96, A:R.113, A:R.113, A:N.123, A:H.126, A:G.127 Hydrogen bonds: A:K.20, A:R.113, A:N.123, A:N.123 Salt bridges: A:R.96 pi-Stacking: A:F.68, A:F.68 IDP.4: 12 residues within 4Å: Chain B: K.20, Y.60, L.63, F.68, L.72, R.96, T.102, V.120, G.121, N.123 Chain D: E.160 Ligands: MG.3 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.20, B:N.123, B:N.123 Water bridges: B:K.20, B:R.113, B:G.127, D:E.160 Salt bridges: B:R.96 pi-Stacking: B:F.68, B:F.68 IDP.6: 12 residues within 4Å: Chain B: E.160 Chain C: K.20, Y.60, L.63, F.68, L.72, R.96, T.102, V.120, G.121, N.123 Ligands: MG.5 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.20, C:N.123, C:N.123 Water bridges: C:K.20, C:R.96, C:R.113, C:R.113, C:H.126, C:H.126, C:H.126, C:H.126, B:E.160 Salt bridges: C:R.96 pi-Stacking: C:F.68, C:F.68 IDP.8: 12 residues within 4Å: Chain C: E.160 Chain D: K.20, Y.60, L.63, F.68, L.72, R.96, T.102, V.120, G.121, N.123 Ligands: MG.7 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.20, D:T.102, D:R.113, D:N.123, D:N.123 Water bridges: D:K.20, D:R.96, D:R.96, D:R.96, D:R.113, D:R.113, D:N.123, D:G.127, C:E.160, C:E.160 Salt bridges: D:R.96 pi-Stacking: D:F.68, D:F.68 IDP.10: 12 residues within 4Å: Chain A: E.160 Chain E: K.20, Y.60, L.63, F.68, L.72, R.96, T.102, V.120, G.121, N.123 Ligands: MG.9 14 PLIP interactions: 13 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:K.20, E:T.102, E:N.123, E:N.123 Water bridges: E:Y.60, E:H.126, E:H.126, E:H.126, E:H.126, E:G.127, A:E.160 Salt bridges: E:R.96 pi-Stacking: E:F.68, E:F.68 IDP.12: 12 residues within 4Å: Chain E: E.160 Chain F: K.20, Y.60, L.63, F.68, L.72, R.96, T.102, V.120, G.121, N.123 Ligands: MG.11 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:K.20, F:T.102, F:N.123, F:N.123 Water bridges: F:K.20, F:R.96, F:R.113, F:R.113, F:G.127, E:E.160 Salt bridges: F:R.96 pi-Stacking: F:F.68, 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
A

E
B

F
C

Nucleoside diphosphate kinase

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