SMTL ID : 7ypj.1

Spiral pentamer of the substrate-free Lon protease with a S678A mutation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: D.318, Y.320, G.321, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, I.501, V.540 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.320, A:G.358, A:V.359, A:G.360, A:K.361, A:T.362, A:T.362, A:T.362, A:Y.493 Salt bridges: A:K.361 ADP.2: 12 residues within 4Å: Chain B: H.319, P.357, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, I.501, Y.505, R.541 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:V.359, B:G.360, B:K.361, B:T.362, B:T.362, B:S.363, B:Y.493, B:Y.493 Salt bridges: B:K.361, B:R.541 pi-Cation interactions: B:H.319, B:H.319 ADP.3: 12 residues within 4Å: Chain C: H.319, P.357, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, I.501, V.540, R.541 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.319, C:P.357, C:K.361, C:T.362, C:S.363, C:S.363, C:Y.493 ADP.4: 16 residues within 4Å: Chain D: D.318, H.319, Y.320, P.357, G.358, V.359, G.360, K.361, T.362, S.363, R.366, Y.493, I.501, Y.505, V.540, R.541 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Y.320, D:G.358, D:V.359, D:G.360, D:K.361, D:T.362, D:S.363, D:S.363, D:S.363, D:R.366, D:R.541 Salt bridges: D:K.361, D:R.541 pi-Stacking: D:H.319 pi-Cation interactions: D:H.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, S. et al., A 5+1 assemble-to-activate mechanism of the Lon proteolytic machine. Nat Commun (2023)

Release Date

2023-10-25

Peptides

Lon protease: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Lon protease

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