SMTL ID : 7ngf.1

P2c-state of wild type human mitochondrial LONP1 protease with bound endogenous substrate protein and in presence of ATP/ADP mix

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: D.368, H.369, Y.370, M.372, P.403, G.404, V.405, G.406, K.407, T.408, S.409, Y.539, I.547, Y.551, L.552, V.587, R.588 Chain B: R.530 Ligands: MG.2 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.369, A:Y.370, A:G.404, A:V.405, A:G.406, A:K.407, A:T.408, A:S.409, A:S.409, A:Y.539 Salt bridges: A:K.407, A:K.407, A:R.588, A:R.588, A:R.588, B:R.530 pi-Cation interactions: A:H.369 ATP.3: 20 residues within 4Å: Chain B: D.368, H.369, Y.370, P.403, G.404, V.405, G.406, K.407, T.408, S.409, Y.539, I.547, Y.551, L.552, V.587, R.588, Q.591 Chain C: Q.493, R.530 Ligands: MG.4 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.370, B:G.404, B:V.405, B:G.406, B:K.407, B:T.408, B:S.409, B:Y.539 Salt bridges: B:K.407, B:K.407, B:R.588, B:R.588, B:R.588, C:R.530 ATP.6: 21 residues within 4Å: Chain D: D.368, H.369, Y.370, P.402, P.403, G.404, V.405, G.406, K.407, T.408, S.409, I.410, Y.539, I.547, Y.551, L.552, Q.555, V.587, R.588, Q.591 Ligands: MG.7 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:H.369, D:Y.370, D:G.404, D:V.405, D:G.406, D:K.407, D:T.408, D:S.409, D:Y.539 Salt bridges: D:K.407, D:K.407, D:R.588 ATP.8: 19 residues within 4Å: Chain E: D.368, H.369, Y.370, M.372, P.403, G.404, V.405, G.406, K.407, T.408, S.409, Y.539, I.547, R.550, Y.551, L.552, Q.555, V.587 Ligands: MG.9 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:Y.370, E:Y.370, E:G.404, E:V.405, E:G.406, E:K.407, E:T.408, E:T.408, E:S.409, E:Y.539 Salt bridges: E:K.407 ATP.10: 24 residues within 4Å: Chain A: E.492, P.526, R.530 Chain F: D.368, H.369, Y.370, M.372, P.402, P.403, G.404, V.405, G.406, K.407, T.408, S.409, E.469, N.518, Y.539, I.547, Y.551, L.552, V.587, R.588 Ligands: MG.11 18 PLIP interactions: 17 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:H.369, F:Y.370, F:G.404, F:V.405, F:G.406, F:K.407, F:T.408, F:S.409, F:S.409, F:E.469, F:N.518, F:Y.539 Salt bridges: F:K.407, F:K.407, F:R.588, F:R.588, F:R.588, A:R.530

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.407, T.408, R.588 Chain B: R.530 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.408 MG.4: 3 residues within 4Å: Chain B: K.407, T.408 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.408 MG.7: 2 residues within 4Å: Chain D: T.408 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.408 MG.9: 2 residues within 4Å: Chain E: T.408 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.408 MG.11: 5 residues within 4Å: Chain A: R.530 Chain F: T.408, D.468, E.469 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.408

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

ADP.5: 18 residues within 4Å: Chain C: D.368, H.369, Y.370, M.372, P.403, G.404, V.405, G.406, K.407, T.408, S.409, I.410, Y.539, I.547, Y.551, L.552, V.587, R.588 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Y.370, C:G.404, C:G.406, C:K.407, C:T.408, C:T.408, C:T.408, C:S.409, C:Y.539 Salt bridges: C:K.407, C:R.588

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mohammed, I. et al., Catalytic cycling of human mitochondrial Lon protease. Structure (2022)

Release Date

2021-04-28

Peptides

Lon protease homolog, mitochondrial: ABCDEF
substrate protein chain:G: 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

substrate protein chain:G

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