SMTL ID : 9cc1.1

Human Mitochondrial LONP1 Idle State bound to substrate and 6 ADP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-6-mer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain B: T.433 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.433 MG.3: 3 residues within 4Å: Chain C: T.433 Chain D: R.555 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.433 MG.5: 4 residues within 4Å: Chain D: T.433, D.493, E.494 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.433 MG.7: 2 residues within 4Å: Chain E: T.433 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.433 MG.10: 3 residues within 4Å: Chain F: T.433, R.613 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.433 MG.12: 2 residues within 4Å: Chain G: T.433 Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

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

ADP.2: 19 residues within 4Å: Chain B: D.393, H.394, Y.395, M.397, P.427, P.428, G.429, V.430, G.431, K.432, T.433, S.434, Y.564, I.572, Y.576, V.612, R.613 Chain C: E.517 Ligands: MG.1 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.395, B:P.427, B:G.429, B:V.430, B:G.431, B:K.432, B:T.433, B:S.434, B:Y.564, C:E.517 Salt bridges: B:K.432, B:R.613, B:R.613 pi-Cation interactions: B:H.394 ADP.4: 15 residues within 4Å: Chain C: D.393, H.394, Y.395, G.429, V.430, G.431, K.432, T.433, S.434, Y.564, I.572, Y.576, R.613 Chain D: E.517 Ligands: MG.3 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Y.395, C:P.427, C:G.429, C:V.430, C:G.431, C:K.432, C:T.433, C:S.434, C:S.434, C:Y.564, C:Y.564, D:E.517 Salt bridges: C:K.432, C:R.613, C:R.613 pi-Cation interactions: C:H.394 ADP.6: 17 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, Y.564, I.572, Y.576, V.612, R.613 Ligands: MG.5 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Y.395, D:P.427, D:G.429, D:V.430, D:G.431, D:K.432, D:T.433, D:T.433, D:S.434, D:S.434, D:Y.564 Salt bridges: D:K.432, D:R.613, D:R.613 pi-Cation interactions: D:H.394, D:H.394 ADP.8: 18 residues within 4Å: Chain E: H.394, Y.395, M.397, P.428, G.429, V.430, G.431, K.432, T.433, S.434, Y.564, I.572, Y.576, Q.580, V.612, R.613 Chain F: E.517 Ligands: MG.7 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:Y.395, E:G.429, E:V.430, E:G.431, E:K.432, E:T.433, E:T.433, E:S.434, E:Y.564, E:Q.580, F:R.555 Salt bridges: E:K.432, E:R.613, E:R.613 pi-Cation interactions: E:H.394 ADP.9: 19 residues within 4Å: Chain F: H.394, Y.395, P.427, P.428, G.429, V.430, G.431, K.432, T.433, S.434, Y.564, I.572, Y.576, L.577, Q.580, V.612, R.613, Q.616 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Y.395, F:G.429, F:V.430, F:G.431, F:K.432, F:T.433, F:S.434, F:S.434, F:S.434, F:Y.564 Salt bridges: F:K.432, F:R.613, F:R.613 pi-Cation interactions: F:H.394 ADP.11: 16 residues within 4Å: Chain G: D.393, H.394, Y.395, M.397, P.428, G.429, V.430, G.431, K.432, T.433, S.434, Y.564, I.572, Y.576, V.612 Ligands: MG.12 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:Y.395, G:Y.395, G:G.429, G:V.430, G:G.431, G:K.432, G:T.433, G:T.433, G:S.434, G:Y.564, G:Q.580 Salt bridges: G:K.432 pi-Stacking: G:H.394, G: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. To Be Published

Release Date

2025-04-30

Peptides

Bound substrate segment undergoing degradation: A
Lon protease homolog, mitochondrial: BCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
A

C
B

D
C

E
D

F
E

G
F

Bound substrate segment undergoing degradation

Lon protease homolog, mitochondrial

Related Entries With Identical Sequence