SMTL ID : 7zl8.2 (1 other biounit)

NME1 in complex with succinyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-hexamer

Ligands

6 x SCA: SUCCINYL-COENZYME A(Non-covalent)

SCA.1: 12 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, I.121, H.122 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.16, A:Y.56, A:Y.56, A:R.109, A:N.119 Water bridges: A:K.16, A:R.92, A:R.92, A:V.116, A:G.123 Salt bridges: A:K.16, A:R.92, A:H.122 pi-Stacking: A:F.64, A:F.64 SCA.2: 11 residues within 4Å: Chain B: K.16, Y.56, L.59, F.64, R.92, T.98, R.109, V.116, N.119, I.121, H.122 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.98, B:R.109, B:N.119 Water bridges: B:K.16, B:K.16, B:R.62, B:T.98, B:G.123 Salt bridges: B:K.16, B:R.92, B:H.122 pi-Stacking: B:F.64, B:F.64 SCA.3: 13 residues within 4Å: Chain C: K.16, Y.56, L.59, R.62, F.64, L.68, R.92, T.98, R.109, V.116, N.119, I.121, H.122 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.16, C:T.98, C:T.98, C:R.109, C:N.119, C:N.119 Water bridges: C:K.16, C:R.92, C:R.92, C:T.98, C:V.116, C:H.122, A:E.156 Salt bridges: C:K.16, C:R.62, C:R.92, C:H.122 pi-Stacking: C:F.64, C:F.64 SCA.4: 13 residues within 4Å: Chain D: K.16, Y.56, L.59, R.62, F.64, L.68, R.92, T.98, R.109, V.116, N.119, I.121, H.122 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:K.16, D:Y.56, D:Y.56, D:R.62, D:T.98, D:R.109, D:N.119 Water bridges: D:G.123, F:E.156 Salt bridges: D:K.16, D:R.92, D:H.122 pi-Stacking: D:F.64, D:F.64 SCA.5: 13 residues within 4Å: Chain E: K.16, Y.56, L.59, R.62, F.64, L.68, R.92, T.98, R.109, V.116, N.119, I.121, H.122 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:K.16, E:Y.56, E:T.98, E:R.109, E:N.119 Water bridges: E:T.98, E:R.109, E:G.123 Salt bridges: E:K.16, E:R.62, E:R.92, E:H.122 pi-Stacking: E:F.64, E:F.64 SCA.6: 13 residues within 4Å: Chain F: K.16, Y.56, L.59, R.62, F.64, L.68, R.92, T.98, R.109, V.116, N.119, I.121, H.122 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:K.16, F:Y.56, F:R.62, F:T.98, F:T.98, F:R.109, F:N.119 Water bridges: F:R.92, F:R.92, F:R.92, F:V.116, F:N.119, F:G.123 Salt bridges: F:K.16, F:R.92, F:H.122 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
G

B
H

C
I

D
J

E
K

F
L

Nucleoside diphosphate kinase A

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