SMTL ID : 7ngc.1

P2a-state of wild type human mitochondrial LONP1 protease with bound substrate protein and in presence of ATPgS

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

5 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 20 residues within 4Å: Chain A: D.384, H.385, Y.386, M.388, P.418, P.419, G.420, V.421, G.422, K.423, T.424, S.425, E.485, Y.555, I.563, Y.567, V.603, R.604 Chain B: R.546 Ligands: MG.2 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.385, A:Y.386, A:Y.386, A:P.418, A:G.420, A:V.421, A:G.422, A:K.423, A:T.424, A:S.425, A:S.425, A:R.604, A:R.604, B:R.546, B:R.546 Salt bridges: A:K.423, A:R.604, A:R.604 pi-Cation interactions: A:H.385 AGS.3: 22 residues within 4Å: Chain B: D.384, H.385, Y.386, M.388, P.418, P.419, G.420, V.421, G.422, K.423, T.424, S.425, E.485, Y.555, I.563, Y.567, L.568, V.603, R.604, Q.607 Chain C: R.546 Ligands: MG.4 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.386, B:Y.386, B:G.420, B:V.421, B:G.422, B:K.423, B:T.424, B:T.424, B:S.425, B:S.425, C:R.546, C:R.546 Salt bridges: B:K.423 pi-Stacking: B:H.385 AGS.5: 19 residues within 4Å: Chain C: D.384, H.385, Y.386, M.388, P.418, P.419, G.420, V.421, G.422, K.423, T.424, S.425, N.534, Y.555, I.563, Y.567, R.604 Chain D: R.546 Ligands: MG.6 15 PLIP interactions: 14 interactions with chain C, 1 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, C:S.425, C:Y.555, D:R.546 Salt bridges: C:K.423 pi-Cation interactions: C:H.385, C:H.385 AGS.8: 20 residues within 4Å: Chain E: H.385, Y.386, M.388, P.418, 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, Q.607 Ligands: MG.9 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:Y.386, E:Y.386, E:G.420, E:V.421, E:G.422, E:K.423, E:T.424, E:T.424, E:S.425, E:S.425, E:R.604 Salt bridges: E:K.423 pi-Stacking: E:Y.567 pi-Cation interactions: E:H.385, E:H.385 AGS.10: 24 residues within 4Å: Chain A: P.542, R.546 Chain F: D.384, H.385, Y.386, M.388, P.418, P.419, G.420, V.421, G.422, K.423, T.424, S.425, E.485, Y.555, I.563, Y.567, L.568, Q.571, V.603, R.604, Q.607 Ligands: MG.11 20 PLIP interactions: 19 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:H.385, F:Y.386, F:Y.386, F:G.420, F:V.421, F:G.422, F:K.423, F:T.424, F:S.425, F:S.425, F:E.485, F:E.485, F:Y.555, F:R.604, F:Q.607, A:R.546 Salt bridges: F:K.423, F:R.604, F:R.604 pi-Cation interactions: F:H.385

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.424, E.485, R.604 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.424 MG.4: 2 residues within 4Å: Chain B: T.424 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.424 MG.6: 2 residues within 4Å: Chain C: T.424 Ligands: AGS.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: AGS.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.424 MG.11: 5 residues within 4Å: Chain A: R.546 Chain F: T.424, E.485, R.604 Ligands: AGS.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.424

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, I.563, Y.567, L.568, Q.571, V.603, R.604, Q.607 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:H.385, D:Y.386, D:Y.386, D:G.420, D:G.422, D:K.423, D:T.424, D:T.424, D:T.424, D:S.425, D:S.425, D:Q.571 Salt bridges: D:K.423

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

2021-04-07

Peptides

Lon protease homolog, mitochondrial: ABCDEF
substrate protein: 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

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