SMTL ID : 9cc0.1

Human Mitochondrial LONP1 Degrading Casein, ATP-bound closed form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 20 residues within 4Å: Chain A: H.394, Y.395, P.427, P.428, G.429, V.430, G.431, K.432, T.433, S.434, E.494, N.543, Y.564, I.572, Y.576, V.612, R.613 Chain B: E.517, R.555 Ligands: MG.2 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.395, A:G.429, A:V.430, A:G.431, A:K.432, A:T.433, A:S.434, A:N.543, A:Y.564, A:Y.564, B:E.517 Salt bridges: A:K.432, A:K.432, A:R.613, A:R.613, A:R.613, B:R.555 pi-Stacking: A:H.394, A:Y.576 ATP.3: 19 residues within 4Å: Chain B: H.394, Y.395, P.428, G.429, V.430, G.431, K.432, T.433, S.434, N.543, Y.564, I.572, Y.576, V.612, R.613, Q.616 Chain C: E.517, R.555 Ligands: MG.4 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.395, B:G.429, B:V.430, B:G.431, B:K.432, B:T.433, B:S.434, B:N.543, B:N.543, B:Y.564, B:Q.616, C:E.517 Salt bridges: B:K.432, B:K.432, B:R.613, B:R.613, B:R.613, C:R.555 pi-Cation interactions: B:H.394, B:H.394 ATP.5: 20 residues within 4Å: Chain C: D.393, H.394, Y.395, P.427, P.428, G.429, V.430, G.431, K.432, T.433, S.434, E.494, N.543, Y.564, I.572, R.613, Q.616 Chain D: E.517, R.555 Ligands: MG.6 23 PLIP interactions: 21 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.395, C:G.429, C:V.430, C:G.431, C:G.431, C:K.432, C:T.433, C:S.434, C:S.434, C:S.434, C:E.494, C:E.494, C:Y.564, C:Q.616, D:E.517 Salt bridges: C:K.432, C:K.432, C:R.613, C:R.613, C:R.613, D:R.555 pi-Cation interactions: C:H.394, C:H.394 ATP.7: 20 residues within 4Å: Chain D: D.393, H.394, Y.395, P.427, P.428, G.429, V.430, G.431, K.432, T.433, S.434, N.543, Y.564, I.572, Y.576, V.612, R.613, Q.616 Chain E: R.555 Ligands: MG.8 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:Y.395, D:G.429, D:V.430, D:G.431, D:K.432, D:T.433, D:S.434, D:Y.564, D:Q.616, D:Q.616 Salt bridges: D:K.432, D:K.432, D:R.613, D:R.613, D:R.613, E:R.555 pi-Cation interactions: D:H.394

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.433, D.493 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.433 MG.4: 3 residues within 4Å: Chain B: T.433, D.493 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.433 MG.6: 4 residues within 4Å: Chain C: T.433, D.493 Chain D: Q.518 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.433, C:D.493 MG.8: 4 residues within 4Å: Chain D: T.433, D.493, T.541 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.433

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

ADP.9: 14 residues within 4Å: Chain E: H.394, Y.395, G.429, V.430, G.431, K.432, T.433, S.434, Y.564, I.572, Y.576, V.612, R.613, Q.616 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:Y.395, E:G.429, E:V.430, E:G.431, E:K.432, E:T.433, E:S.434, E:Y.564, E:Y.564, E:R.613 Salt bridges: E:K.432 pi-Cation interactions: E:H.394 ADP.10: 14 residues within 4Å: Chain F: H.394, Y.395, P.428, G.429, V.430, G.431, K.432, T.433, S.434, Y.564, I.572, Y.576, Q.580, V.612 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:Y.395, F:Y.395, F:G.429, F:V.430, F:G.431, F:K.432, F:T.433, F:S.434, F:Y.564, F:Q.580, F:Q.580 pi-Stacking: F:Y.576

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mindrebo, J.T. et al., Structural and mechanistic studies on human LONP1 redefine the hand-over-hand translocation mechanism. Biorxiv (2024)

Release Date

2024-08-07

Peptides

Lon protease homolog, mitochondrial: ABCDEF
Bound substrate segment undergoing translocation and subsequent degradation: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Lon protease homolog, mitochondrial

Bound substrate segment undergoing translocation and subsequent degradation

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