SMTL ID : 9cc3.1

Human Mitochondrial LONP1 Stall State + casein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-6-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain C: 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.2 15 PLIP interactions: 15 interactions with chain C 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 Salt bridges: C:K.432, C:R.613, C:R.613 pi-Stacking: C:H.394, C:H.394 ADP.3: 17 residues within 4Å: Chain D: D.393, H.394, Y.395, M.397, G.429, V.430, G.431, K.432, T.433, S.434, Y.564, I.572, Y.576, Q.580, V.612, R.613 Ligands: MG.4 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:S.434, D:Y.564, D:Y.564, D:Q.580 Salt bridges: D:K.432, D:R.613, D:R.613 pi-Stacking: D:Y.576 pi-Cation interactions: D:H.394 ADP.5: 17 residues within 4Å: Chain E: D.393, H.394, Y.395, 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 F: E.517, R.555 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:T.433, E:S.434, E:Y.564 Salt bridges: E:K.432, E:R.613, E:R.613, F:R.555 pi-Cation interactions: E:H.394 ADP.7: 17 residues within 4Å: Chain F: 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, Q.616 Ligands: MG.8 15 PLIP interactions: 15 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:T.433, F:S.434, F:Y.564, F:Q.580, F:Q.580, F:R.613, F:Q.616 Salt bridges: F:K.432 pi-Cation interactions: F:H.394

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain C: T.433 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.433 MG.4: 3 residues within 4Å: Chain D: T.433 Chain E: R.555 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.433 MG.6: 3 residues within 4Å: Chain E: R.449, D.493, E.494 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.493, E:E.494 MG.8: 3 residues within 4Å: Chain F: T.433, R.613 Ligands: ADP.7 No protein-ligand interaction detected (PLIP)

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

Endogenous Co-purified substrate modeled as unknown residues: 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

Endogenous Co-purified substrate modeled as unknown residues

Lon protease homolog, mitochondrial

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