SMTL ID : 7fid.1

Processive cleavage of substrate at individual proteolytic active sites of the Lon proteasecomplex (conformation 1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

3 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 15 residues within 4Å: Chain A: H.319, Y.320, P.357, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, I.501, V.540, R.541 Chain B: E.446, R.484 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.319, A:Y.320, A:G.360, A:K.361, A:T.362, A:S.363, A:S.363, A:S.363, A:Y.493, A:R.541, B:E.446, B:R.484, B:R.484 Salt bridges: A:K.361, A:R.541, A:R.541 pi-Stacking: A:H.319 AGS.2: 17 residues within 4Å: Chain B: H.319, Y.320, P.357, G.358, V.359, G.360, K.361, T.362, S.363, E.423, N.472, Y.493, I.501, V.540, R.541 Chain C: E.446, R.484 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.320, B:Y.320, B:G.358, B:K.361, B:K.361, B:T.362, B:T.362, B:S.363, B:E.423, B:E.423, B:N.472, C:R.484 Salt bridges: B:K.361, B:R.541, B:R.541 pi-Stacking: B:H.319, B:H.319 AGS.6: 17 residues within 4Å: Chain A: E.446, R.484 Chain F: H.319, Y.320, P.357, G.358, V.359, G.360, K.361, T.362, S.363, N.472, Y.493, I.501, Y.505, V.540, R.541 20 PLIP interactions: 17 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:H.319, F:Y.320, F:G.360, F:K.361, F:T.362, F:T.362, F:T.362, F:S.363, F:S.363, F:S.363, F:Y.493, F:R.541, F:R.541, A:E.446, A:E.446, A:R.484 Salt bridges: F:K.361, F:R.541, F:R.541 pi-Stacking: F:H.319

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

ADP.3: 15 residues within 4Å: Chain C: H.319, Y.320, P.357, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, I.501, K.509, V.540, R.541, E.544 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Y.320, C:Y.320, C:G.358, C:V.359, C:G.360, C:K.361, C:T.362, C:S.363, C:K.509 Salt bridges: C:K.361, C:R.541, C:R.541 pi-Cation interactions: C:H.319, C:H.319 ADP.4: 14 residues within 4Å: Chain D: D.318, H.319, Y.320, L.322, P.357, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, Y.505, V.540 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:Y.320, D:Y.320, D:G.358, D:G.360, D:K.361, D:T.362, D:T.362, D:S.363 pi-Stacking: D:H.319, D:Y.505 ADP.5: 13 residues within 4Å: Chain E: H.319, Y.320, P.356, P.357, G.358, V.359, G.360, K.361, T.362, Y.493, I.501, Y.505, R.541 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:Y.320, E:P.356, E:G.358, E:V.359, E:K.361, E:T.362, E:T.362, E:R.541 Salt bridges: E:K.361, E:R.541

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, S. et al., Processive cleavage of substrate at individual proteolytic active sites of the Lon protease complex. Sci Adv (2021)

Release Date

2021-11-24

Peptides

Lon protease: ABCDEF
unknown endogenous substrate: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

F
A

G
S

Lon protease

unknown endogenous substrate

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