SMTL ID : 7ksm.1

Human mitochondrial LONP1 with endogenous substrate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: H.76, Y.77, M.79, P.110, G.111, V.112, G.113, K.114, T.115, S.116, Y.246, I.254, Y.258, V.294, R.295 Chain B: E.199, P.233, R.237 Ligands: MG.2 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.77, A:G.111, A:V.112, A:G.113, A:K.114, A:T.115, A:S.116, A:S.116, A:S.116, A:Y.246, A:Y.246, B:E.199 Salt bridges: A:K.114, A:K.114, A:R.295, A:R.295, A:R.295, B:R.237 pi-Stacking: A:H.76 ATP.3: 17 residues within 4Å: Chain B: H.76, Y.77, P.110, G.111, V.112, G.113, K.114, T.115, S.116, E.176, Y.246, I.254, Y.258, R.295 Chain C: E.199, R.237 Ligands: MG.4 18 PLIP interactions: 2 interactions with chain C, 16 interactions with chain B Hydrogen bonds: C:E.199, B:Y.77, B:G.111, B:V.112, B:G.113, B:K.114, B:T.115, B:T.115, B:S.116, B:Y.246, B:Y.246 Salt bridges: C:R.237, B:K.114, B:K.114, B:R.295, B:R.295, B:R.295 pi-Cation interactions: B:H.76 ATP.6: 21 residues within 4Å: Chain C: D.75, H.76, Y.77, G.78, M.79, P.110, G.111, V.112, G.113, K.114, T.115, S.116, E.176, Y.246, I.254, Y.258, V.294, R.295 Chain D: E.199, R.237 Ligands: MG.5 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.77, C:G.78, C:G.111, C:K.114, C:T.115, C:S.116, C:S.116, C:S.116, C:Y.246, C:Y.246, D:E.199 Salt bridges: C:K.114, C:K.114, C:R.295, C:R.295, C:R.295, D:R.237 pi-Cation interactions: C:H.76 ATP.7: 21 residues within 4Å: Chain D: D.75, H.76, Y.77, M.79, P.110, G.111, V.112, G.113, K.114, T.115, S.116, E.176, N.225, Y.246, I.254, V.294, R.295, Q.298 Chain E: E.199, R.237 Ligands: MG.8 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:Y.77, D:G.111, D:V.112, D:G.113, D:K.114, D:T.115, D:S.116, D:E.176, D:Y.246, D:Q.298, E:E.199 Salt bridges: D:K.114, D:K.114, D:R.295, D:R.295, D:R.295, E:R.237 pi-Cation interactions: D:H.76

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.115, D.175 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.115 MG.4: 4 residues within 4Å: Chain B: T.115, E.176 Chain C: R.237 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.115 MG.5: 5 residues within 4Å: Chain C: T.115, D.175, E.176 Chain D: R.237 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.115 MG.8: 4 residues within 4Å: Chain D: T.115, D.175 Chain E: R.237 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.115

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

ADP.9: 17 residues within 4Å: Chain E: D.75, H.76, Y.77, M.79, P.110, G.111, V.112, G.113, K.114, T.115, S.116, Y.246, I.254, Y.258, V.294, R.295, Q.298 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:Y.77, E:G.111, E:V.112, E:G.113, E:K.114, E:T.115, E:T.115, E:T.115, E:S.116, E:S.116, E:Y.246, E:Q.298 Salt bridges: E:K.114, E:R.295, E:R.295 pi-Cation interactions: E:H.76 ADP.10: 16 residues within 4Å: Chain F: H.76, Y.77, M.79, P.110, G.111, V.112, G.113, K.114, T.115, S.116, Y.246, I.254, Y.258, Q.262, V.294, Q.298 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:Y.77, F:Y.77, F:G.111, F:G.113, F:K.114, F:T.115, F:T.115, F:T.115, F:Q.262 Salt bridges: F:K.114, F:K.114 pi-Stacking: F:H.76, F:Y.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, M. et al., Structures of the human LONP1 protease reveal regulatory steps involved in protease activation. Nat Commun (2021)

Release Date

2020-12-02

Peptides

Lon protease homolog, mitochondrial: ABCDEF
Unidentified endogenous substrate: 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

Unidentified endogenous substrate

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