SMTL ID : 8k3y.1

The "5+1" heteromeric structure of Lon protease consisting of a spiral pentamer with Y224S mutation and an N-terminal-truncated monomeric E613K mutant

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-1-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain B: D.318, H.319, Y.320, P.356, P.357, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, I.501, Y.505, L.506, V.540, E.544 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:H.319, B:G.358, B:V.359, B:G.360, B:K.361, B:T.362, B:T.362, B:T.362, B:S.363, B:S.363, B:S.363 Salt bridges: B:K.361 pi-Stacking: B:H.319 ADP.2: 18 residues within 4Å: Chain C: D.318, H.319, Y.320, G.321, P.357, G.358, V.359, G.360, K.361, T.362, S.363, R.378, Y.493, I.501, Y.505, L.506, V.540, R.541 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:Y.320, C:G.321, C:G.360, C:K.361, C:T.362, C:S.363, C:S.363, C:S.363, C:R.378, C:Y.493 Salt bridges: C:K.361, C:R.378, C:R.541, C:R.541 pi-Stacking: C:H.319, C:H.319 ADP.3: 18 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, K.509, V.540, R.541, E.544 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:D.318, D:H.319, D:Y.320, D:K.361, D:T.362, D:T.362, D:T.362, D:S.363, D:S.363, D:R.366, D:R.366, D:K.509 Salt bridges: D:K.361, D:K.361, D:R.541, D:R.541 ADP.4: 19 residues within 4Å: Chain E: H.319, P.356, P.357, G.358, V.359, G.360, K.361, T.362, S.363, L.364, R.378, E.423, Y.493, I.501, Y.505, L.506, V.540, R.541, E.544 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:H.319, E:V.359, E:K.361, E:T.362, E:T.362, E:T.362, E:S.363, E:S.363, E:E.423, E:Y.493, E:R.541, E:R.541 Salt bridges: E:K.361, E:R.378, E:R.541

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
Lon protease: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Lon protease

Lon protease