SMTL ID : 7ng5.1

P1c-state of wild type human mitochondrial LONP1 protease with bound substrate protein in presence of ATP/ADP mix

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: D.384, H.385, Y.386, M.388, P.419, G.420, V.421, G.422, K.423, T.424, S.425, E.485, N.534, Y.555, I.563, Y.567, L.568, Q.571, V.603, R.604 Chain B: E.508, P.542, R.546 Ligands: MG.2 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.385, A:Y.386, A:G.420, A:V.421, A:G.422, A:K.423, A:T.424, A:S.425, A:N.534, A:Y.555, A:Y.555, B:E.508 Salt bridges: A:K.423, A:K.423, A:R.604, A:R.604, B:R.546 ATP.3: 21 residues within 4Å: Chain B: H.385, Y.386, M.388, P.419, G.420, V.421, G.422, K.423, T.424, S.425, N.534, Y.555, I.563, Y.567, L.568, V.603, R.604 Chain C: E.508, P.542, R.546 Ligands: MG.4 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.386, B:G.420, B:V.421, B:G.422, B:K.423, B:T.424, B:S.425, B:N.534, B:Y.555, B:Y.555 Salt bridges: B:K.423, B:K.423, B:K.423, B:R.604, C:R.546 pi-Cation interactions: B:H.385 ATP.5: 21 residues within 4Å: Chain C: D.384, H.385, Y.386, P.419, G.420, V.421, G.422, K.423, T.424, S.425, Y.555, I.563, Y.567, L.568, V.603, R.604, Q.607 Chain D: D.506, E.508, R.546 Ligands: MG.6 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.386, C:Y.386, C:G.420, C:V.421, C:G.422, C:K.423, C:T.424, C:T.424, C:S.425, D:E.508 Salt bridges: C:K.423, C:K.423, C:R.604, D:R.546 ATP.8: 19 residues within 4Å: Chain E: H.385, Y.386, M.388, P.419, G.420, V.421, G.422, K.423, T.424, S.425, N.534, Y.555, I.563, Y.567, L.568, Q.571, R.604, Q.607 Ligands: MG.9 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.420, E:V.421, E:G.422, E:K.423, E:T.424, E:T.424, E:S.425, E:Y.555 Salt bridges: E:K.423, E:K.423, E:R.604 pi-Stacking: E:H.385 ATP.10: 18 residues within 4Å: Chain F: D.384, H.385, Y.386, M.388, P.419, G.420, V.421, G.422, K.423, T.424, S.425, Y.555, I.563, Y.567, L.568, Q.571, V.603 Ligands: MG.11 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:Y.386, F:G.420, F:G.422, F:K.423, F:T.424, F:T.424, F:S.425, F:S.425, F:Y.555, F:Q.571 Salt bridges: F:K.423, F:K.423 pi-Stacking: F:Y.567

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.424, E.485 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.424 MG.4: 3 residues within 4Å: Chain B: T.424 Chain C: R.546 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.424 MG.6: 3 residues within 4Å: Chain C: K.423, T.424 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.424 MG.9: 2 residues within 4Å: Chain E: T.424 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain F: T.424 Ligands: ATP.10 No protein-ligand interaction detected (PLIP)

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

ADP.7: 18 residues within 4Å: Chain D: D.384, H.385, Y.386, M.388, P.419, G.420, V.421, G.422, K.423, T.424, S.425, Y.555, I.563, Y.567, L.568, Q.571, V.603, R.604 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Y.386, D:G.420, D:G.422, D:K.423, D:T.424, D:T.424, D:S.425, D:S.425, D:Y.555, D:Y.555 Salt bridges: D:K.423, D:R.604

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

2021-02-24

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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