SMTL ID : 7zlw.1

NME1 in complex with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 10 residues within 4Å: Chain A: K.16, Y.56, L.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.16, A:R.109, A:N.119, A:N.119 Water bridges: A:K.16, A:R.92, A:R.92, A:T.98, A:H.122, A:G.123, A:D.125 Salt bridges: A:R.92, A:R.109 pi-Stacking: A:F.64, A:F.64 ADP.2: 12 residues within 4Å: Chain B: K.16, Y.56, L.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Chain C: E.156 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:K.16, B:R.109, B:N.119, B:N.119 Water bridges: B:K.16, B:R.62, B:R.92, B:R.92, B:R.92, B:R.92, B:T.98, B:G.123 Salt bridges: B:R.92, B:R.109 pi-Stacking: B:F.64, B:F.64 ADP.3: 12 residues within 4Å: Chain A: E.156 Chain C: K.16, Y.56, L.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.16, C:R.109, C:N.119, C:N.119 Water bridges: C:K.16, C:Y.56, C:R.92, C:R.92 Salt bridges: C:R.92, C:R.109 pi-Stacking: C:F.64, C:F.64 ADP.4: 11 residues within 4Å: Chain D: K.16, Y.56, L.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.16, D:N.119, D:N.119 Water bridges: D:K.16, D:R.92, D:R.109, D:H.122 Salt bridges: D:R.92, D:R.109 pi-Stacking: D:F.64, D:F.64 ADP.5: 12 residues within 4Å: Chain E: E.156 Chain F: K.16, Y.56, L.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:K.16, F:R.109, F:N.119, F:N.119 Water bridges: F:K.16, F:R.92, F:R.92, F:R.92, F:R.92, F:R.92, F:H.122 Salt bridges: F:R.92, F:R.109 pi-Stacking: F:F.64, F:F.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iuso, D. et al., Nucleoside diphosphate kinases 1 and 2 regulate a protective liver response to a high-fat diet. Sci Adv (2023)

Release Date

2023-08-09

Peptides

Nucleoside diphosphate kinase A: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleoside diphosphate kinase A

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