SMTL ID : 7fd4.1

A complete three-dimensional structure of the Lon protease translocating a protein substrate (conformation 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

AGS.1: 16 residues within 4Å: Chain A: H.319, Y.320, P.357, G.358, V.359, G.360, K.361, T.362, S.363, E.423, Y.493, I.501, V.540, R.541 Chain B: E.446, R.484 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.320, A:G.360, A:K.361, A:K.361, A:T.362, A:T.362, A:S.363, A:S.363, A:S.363, A:E.423, A:Y.493, A:Y.493, A:R.541, B:R.484, B:R.484 Salt bridges: A:K.361, A:R.541, A:R.541 pi-Stacking: A:H.319, A:Y.505 AGS.3: 18 residues within 4Å: Chain B: D.318, 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 18 PLIP interactions: 16 interactions with chain B, 2 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:E.423, C:E.446, C:R.484 Salt bridges: B:K.361, B:R.541, B:R.541 pi-Cation interactions: B:H.319, B:H.319 AGS.9: 14 residues within 4Å: Chain E: Y.320, L.322, P.356, P.357, G.358, V.359, G.360, K.361, T.362, Y.493, I.501, Y.505, V.540, R.541 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:Y.320, E:Y.320, E:P.356, E:G.358, E:V.359, E:K.361, E:T.362, E:N.472, E:Y.493, E:R.541, E:R.541 Salt bridges: E:K.361, E:R.541 pi-Stacking: E:H.319 AGS.11: 17 residues within 4Å: Chain A: E.446, R.484 Chain F: H.319, Y.320, P.357, V.359, G.360, K.361, T.362, S.363, E.423, N.472, Y.493, I.501, Y.505, V.540, R.541 20 PLIP interactions: 18 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:Y.320, F:V.359, F:G.360, F:K.361, F:K.361, F:T.362, F:T.362, F:S.363, F:S.363, F:S.363, F:N.472, F:Y.493, F:Y.493, F:R.541, A:E.446, A:R.484 Salt bridges: F:K.361, F:R.541, F:R.541 pi-Stacking: F:H.319

6 x 4KZ: N-[(1R)-1-(dihydroxyboranyl)-2-phenylethyl]-Nalpha-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide(Covalent)

4KZ.2: 13 residues within 4Å: Chain A: A.601, W.602, T.603, L.610, M.633, P.673, K.674, D.675, G.676, P.677, S.678, A.679, K.721 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.601, A:L.610, A:A.679 Hydrogen bonds: A:W.602, A:W.602, A:D.675, A:D.675, A:G.676, A:S.678, A:A.679, A:K.721 4KZ.4: 15 residues within 4Å: Chain B: L.600, A.601, W.602, T.603, L.610, M.633, P.673, K.674, D.675, G.676, P.677, S.678, A.679, G.716, K.721 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.601, B:W.602, B:L.610, B:A.679 Hydrogen bonds: B:W.602, B:D.675, B:D.675, B:S.678, B:K.721 4KZ.6: 15 residues within 4Å: Chain C: L.600, A.601, W.602, T.603, L.610, M.633, T.672, P.673, K.674, D.675, G.676, P.677, S.678, A.679, K.721 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.601, C:L.610, C:K.674, C:A.679 Hydrogen bonds: C:W.602, C:W.602, C:D.675, C:D.675, C:D.675, C:S.678, C:K.721 4KZ.8: 13 residues within 4Å: Chain D: A.601, W.602, T.603, L.610, M.633, P.673, K.674, D.675, G.676, P.677, S.678, A.679, K.721 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:A.601, D:W.602, D:L.610, D:A.679 Hydrogen bonds: D:W.602, D:W.602, D:D.675, D:S.678, D:K.721 4KZ.10: 14 residues within 4Å: Chain E: L.600, A.601, W.602, T.603, L.610, M.633, T.672, P.673, K.674, D.675, G.676, P.677, S.678, K.721 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:A.601, E:L.610 Hydrogen bonds: E:W.602, E:W.602, E:D.675, E:D.675, E:S.678, E:K.721 4KZ.12: 14 residues within 4Å: Chain F: A.601, W.602, T.603, T.608, L.610, T.672, P.673, K.674, D.675, G.676, P.677, S.678, A.679, K.721 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:L.610, F:K.674, F:A.679 Hydrogen bonds: F:W.602, F:W.602, F:D.675, F:D.675, F:S.678, F:K.721

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

ADP.5: 14 residues within 4Å: Chain C: H.319, Y.320, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, L.506, K.509, V.540, R.541, E.544 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:T.362, C:S.363 Salt bridges: C:K.361, C:R.541 pi-Cation interactions: C:H.319, C:H.319 ADP.7: 15 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, I.501, Y.505, V.540 11 PLIP interactions: 11 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:T.362, D:S.363, D:Y.493 pi-Stacking: D:H.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, S. et al., Complete three-dimensional structures of the Lon protease translocating a protein substrate. Sci Adv (2021)

Release Date

2021-11-03

Peptides

Lon protease: ABCDEF
Alpha-S1-casein: 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

Alpha-S1-casein

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