SMTL ID : 7fd5.1

A complete three-dimensional structure of the Lon protease translocating a protein substrate (conformation 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: Y.320, P.356, P.357, G.358, V.359, G.360, K.361, T.362, Y.493, I.501, Y.505, V.540, R.541, E.544 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.320, A:Y.320, A:G.358, A:V.359, A:K.361, A:T.362, A:T.362 Salt bridges: A:K.361, A:R.541, A:R.541 ADP.5: 14 residues within 4Å: Chain C: D.318, H.319, Y.320, P.357, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, 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:K.361, C:T.362, C:T.362, C:S.363, C:Y.493 Salt bridges: C:K.361, C:R.541, C:R.541 pi-Cation interactions: C:H.319, C:H.319 ADP.9: 16 residues within 4Å: Chain E: H.319, Y.320, P.357, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, I.501, Y.505, L.506, K.509, V.540, R.541 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:Y.320, E:Y.320, E:G.358, E:K.361, E:T.362, E:T.362, E:T.362, E:S.363, E:Y.493, E:K.509, E:R.541 Salt bridges: E:K.361, E:R.541 pi-Cation interactions: E: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 8 PLIP interactions: 8 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:S.678, A:K.721 4KZ.4: 14 residues within 4Å: Chain B: A.601, W.602, T.608, L.610, M.633, 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 B Hydrophobic interactions: B:L.610, B:K.674, B:A.679 Hydrogen bonds: B:W.602, 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, 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 C Hydrophobic interactions: C:A.601, C:L.610, C:A.679 Hydrogen bonds: C:W.602, C:W.602, 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 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:A.601, D:L.610, D:A.679 Hydrogen bonds: D:W.602, D:W.602, D:D.675, D:D.675, D:G.676, D:S.678, D:A.679, D:K.721 4KZ.10: 15 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, A.679, K.721 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:A.601, E:L.610, E:K.674, E:A.679 Hydrogen bonds: E:W.602, E:W.602, E:D.675, E:D.675, E:D.675, E:S.678, E:K.721 4KZ.12: 15 residues within 4Å: Chain F: L.600, A.601, W.602, T.603, T.608, 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 F Hydrophobic interactions: F:W.602, F:L.610 Hydrogen bonds: F:W.602, F:W.602, F:D.675, F:D.675, F:S.678, F:K.721

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

AGS.3: 19 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, Y.505, V.540, R.541 Chain D: E.446, R.484 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:Y.320, B:K.361, B:K.361, B:T.362, B:S.363, B:S.363, B:S.363, B:N.472, B:Y.493, B:Y.493, B:R.541, D:E.446, D:R.484, D:R.484 Salt bridges: B:K.361, B:R.541, B:R.541 pi-Stacking: B:H.319 AGS.7: 14 residues within 4Å: Chain C: R.484 Chain D: D.318, H.319, Y.320, G.358, V.359, G.360, K.361, T.362, S.363, Y.493, I.501, V.540, R.541 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.320, D:G.358, D:G.360, D:K.361, D:K.361, D:T.362, D:T.362, D:S.363, D:S.363, D:Y.493, D:Y.493, D:R.541, C:R.484 Salt bridges: D:K.361, D:R.541, D:R.541 pi-Stacking: D:H.319 pi-Cation interactions: D:H.319 AGS.11: 18 residues within 4Å: Chain B: E.446, P.480, 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: 19 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:Y.320, F:G.358, F:G.360, F:K.361, F:K.361, F:T.362, F:T.362, F:T.362, F:S.363, F:S.363, F:S.363, F:N.472, F:Y.493, F:R.541, F:R.541, B:R.484 Salt bridges: F:K.361, F:R.541, F:R.541 pi-Stacking: F: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
F

B
B

C
D

D
C

E
E

F
A

G
S

Lon protease

Alpha-S1-casein

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