SMTL ID : 6wqh.1

Molecular basis for the ATPase-powered substrate translocation by the Lon AAA+ protease

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

AGS.1: 17 residues within 4Å: Chain A: H.320, Y.321, P.358, V.360, G.361, K.362, T.363, D.423, E.424, T.471, Y.494, I.502, Y.506, V.541, R.542 Chain B: E.447, R.485 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.321, A:G.361, A:K.362, A:T.363, A:E.424, A:Y.494, B:R.485 Salt bridges: A:R.542, A:R.542, B:R.485 AGS.3: 17 residues within 4Å: Chain B: H.320, Y.321, P.358, G.359, V.360, G.361, K.362, T.363, S.364, E.424, Y.494, I.502, V.541, R.542 Chain C: E.447, P.481, R.485 18 PLIP interactions: 2 interactions with chain C, 16 interactions with chain B Hydrogen bonds: C:R.485, C:R.485, B:Y.321, B:Y.321, B:G.359, B:K.362, B:K.362, B:T.363, B:T.363, B:T.363, B:S.364, B:S.364, B:S.364, B:E.424 Salt bridges: B:K.362, B:K.362, B:R.542, B:R.542 AGS.5: 13 residues within 4Å: Chain C: Y.321, P.358, G.359, V.360, G.361, K.362, T.363, S.364, N.473, Y.494, I.502, R.542 Chain E: R.485 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:Y.321, C:G.359, C:G.361, C:K.362, C:K.362, C:T.363, C:T.363, C:T.363, C:S.364, C:N.473, C:Y.494, E:R.485 Salt bridges: C:K.362, C:R.542, C:R.542 pi-Stacking: C:H.320

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

4KZ.2: 14 residues within 4Å: Chain A: A.602, W.603, T.604, T.609, L.611, P.674, K.675, D.676, G.677, P.678, S.679, A.680, I.716, K.722 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.602, A:L.611, A:D.676, A:A.680 Hydrogen bonds: A:W.603, A:W.603, A:D.676, A:S.679, A:K.722 4KZ.4: 13 residues within 4Å: Chain B: L.601, A.602, W.603, T.604, L.611, T.673, P.674, K.675, D.676, G.677, P.678, S.679, K.722 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.602, B:W.603, B:L.611 Hydrogen bonds: B:W.603, B:W.603, B:T.673, B:D.676, B:S.679, B:K.722 4KZ.6: 15 residues within 4Å: Chain C: L.601, A.602, W.603, T.604, T.609, L.611, M.634, K.675, D.676, G.677, P.678, S.679, A.680, I.716, K.722 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.602, C:L.611, C:A.680 Hydrogen bonds: C:W.603, C:W.603, C:D.676, C:D.676, C:K.722 4KZ.8: 13 residues within 4Å: Chain D: L.601, A.602, W.603, T.609, L.611, M.634, P.674, K.675, D.676, G.677, P.678, S.679, A.680 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:A.602, D:L.611, D:A.680 Hydrogen bonds: D:W.603, D:W.603, D:T.609, D:D.676, D:D.676, D:D.676, D:S.679 4KZ.10: 15 residues within 4Å: Chain E: L.601, A.602, W.603, T.604, L.611, I.613, M.634, T.673, K.675, D.676, G.677, P.678, S.679, A.680, K.722 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:A.602, E:L.611, E:I.613, E:D.676, E:A.680 Hydrogen bonds: E:W.603, E:W.603, E:D.676, E:D.676, E:G.677, E:S.679, E:A.680, E:K.722 4KZ.11: 13 residues within 4Å: Chain F: L.601, A.602, W.603, T.604, L.611, M.634, K.675, D.676, G.677, P.678, S.679, A.680, K.722 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:A.602, F:L.611, F:A.680 Hydrogen bonds: F:W.603, F:W.603, F:D.676, F:S.679, F:K.722

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

ADP.7: 14 residues within 4Å: Chain D: D.319, H.320, Y.321, P.358, G.359, V.360, G.361, K.362, T.363, Y.494, I.502, Y.506, V.541, R.542 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:H.320, D:Y.321, D:K.362, D:T.363, D:Y.494, D:Y.494 Salt bridges: D:R.542, D:R.542 ADP.9: 16 residues within 4Å: Chain E: H.320, Y.321, P.357, P.358, G.359, V.360, G.361, K.362, T.363, S.364, Y.494, I.502, Y.506, L.507, R.542 Chain F: R.480 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:Y.321, E:G.359, E:G.361, E:K.362, E:T.363, E:S.364, E:Y.494, F:R.480 Salt bridges: E:K.362 pi-Stacking: E:H.320 pi-Cation interactions: E:H.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, S. et al., Molecular basis for ATPase-powered substrate translocation by the Lon AAA+ protease. J.Biol.Chem. (2021)

Release Date

2021-06-09

Peptides

Lon protease: ABCDEF
Ig2 substrate: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
D

F
E

G
S

Lon protease

Ig2 substrate

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