SMTL ID : 7ypk.1

Close-ring hexamer of the substrate-bound Lon protease with an S678A mutation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-6-mer

Ligands

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

ADP.1: 19 residues within 4Å: Chain B: 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, V.540, R.541 Chain C: D.444, E.446, Q.447, R.484 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.320, B:Y.320, B:G.360, B:K.361, B:T.362, B:T.362, B:T.362, B:S.363, C:E.446, C:Q.447 Salt bridges: B:K.361, B:R.541 pi-Cation interactions: B:H.319 ADP.2: 16 residues within 4Å: Chain C: D.318, H.319, Y.320, L.322, P.356, P.357, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, I.501, V.540, R.541 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.320, C:Y.320, C:G.358, C:G.360, C:K.361, C:T.362, C:T.362, C:S.363, C:S.363, C:Y.493 Salt bridges: C:K.361 pi-Stacking: C:H.319, C:H.319 ADP.3: 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.378, Y.493, I.501, Y.505, V.540, R.541 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Y.320, D:G.358, D:K.361, D:T.362, D:T.362, D:T.362, D:S.363, D:S.363, D:S.363, D:R.378, D:Y.493, D:Y.493 Salt bridges: D:K.361 ADP.4: 15 residues within 4Å: Chain E: H.319, Y.320, L.322, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, I.501, Y.505, L.506, V.540, R.541 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:Y.320, E:Y.320, E:G.358, E:G.360, E:K.361, E:T.362, E:T.362, E:T.362, E:S.363, E:Y.493, E:R.541, E:R.541 Salt bridges: E:K.361, E:R.541 pi-Cation interactions: E:H.319, E:H.319 ADP.5: 16 residues within 4Å: Chain F: H.319, Y.320, L.322, 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 F Hydrogen bonds: F:Y.320, F:Y.320, F:G.358, F:V.359, F:G.360, F:K.361, F:T.362, F:T.362, F:T.362, F:S.363, F:R.366 Salt bridges: F:K.361, F:R.541, F:R.541 pi-Stacking: F:H.319 ADP.6: 17 residues within 4Å: Chain B: D.444, E.446 Chain G: D.318, H.319, Y.320, P.357, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, I.501, Y.505, V.540, R.541 13 PLIP interactions: 11 interactions with chain G, 2 interactions with chain B Hydrogen bonds: G:Y.320, G:Y.320, G:P.357, G:V.359, G:K.361, G:T.362, G:T.362, G:T.362, G:S.363, B:E.446, B:E.446 Salt bridges: G:R.541, G: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

alpha-S1-casein: A
Lon protease: BCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
F

C
A

D
B

E
C

F
D

G
E

alpha-S1-casein

Lon protease

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