SMTL ID : 7sxo.1

Yeast Lon (PIM1) with endogenous substrate

Coordinates

PDB Format

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.435, Y.436, G.437, M.438, P.469, G.470, V.471, G.472, K.473, T.474, S.475, Y.606, I.614, Y.618, V.654, R.655 Chain F: E.559, Q.560, R.597 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:Y.436, A:G.437, A:G.470, A:V.471, A:G.472, A:K.473, A:T.474, A:T.474, A:S.475, A:S.475, A:S.475, A:Y.606, A:Y.606, F:E.559, F:E.559 Salt bridges: A:K.473, A:K.473, A:R.655, A:R.655, A:R.655, F:R.597 pi-Cation interactions: A:H.435 ATP.5: 21 residues within 4Å: Chain C: D.596 Chain D: D.434, H.435, Y.436, G.437, P.468, P.469, G.470, V.471, G.472, K.473, T.474, S.475, D.534, Y.606, I.614, Y.618, V.654, R.655, K.658 Ligands: MG.6 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Y.436, D:G.437, D:G.470, D:V.471, D:G.472, D:K.473, D:T.474, D:T.474, D:T.474, D:S.475, D:S.475, D:S.475, D:R.490, D:D.534, D:Y.606, D:R.655 Salt bridges: D:K.473, D:K.473 pi-Cation interactions: D:H.435 ATP.7: 17 residues within 4Å: Chain E: D.434, H.435, Y.436, P.469, G.470, V.471, G.472, K.473, T.474, S.475, D.534, N.585, Y.606, I.614, V.654, R.655, K.658 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:Y.436, E:G.437, E:G.470, E:V.471, E:G.472, E:K.473, E:T.474, E:T.474, E:T.474, E:S.475, E:D.534, E:Y.606, E:Y.606, E:K.658, E:K.658 Salt bridges: E:K.473, E:K.473, E:R.655, E:R.655, E:R.655 pi-Cation interactions: E:H.435 ATP.10: 17 residues within 4Å: Chain E: R.597 Chain F: H.435, Y.436, M.438, P.469, G.470, V.471, G.472, K.473, T.474, S.475, N.585, Y.606, I.614, V.654, R.655, K.658 18 PLIP interactions: 17 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Y.436, F:G.470, F:V.471, F:G.472, F:K.473, F:T.474, F:T.474, F:S.475, F:S.475, F:S.475, F:N.585 Salt bridges: F:K.473, F:K.473, F:R.655, F:R.655, F:R.655, E:R.597 pi-Cation interactions: F:H.435

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: S.492, G.494, G.495 Chain F: E.554 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.492 MG.6: 5 residues within 4Å: Chain D: K.473, T.583, A.584, N.585 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain E: S.622 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

ADP.3: 13 residues within 4Å: Chain A: R.597 Chain B: H.435, P.469, G.470, V.471, G.472, K.473, T.474, I.614, L.619, V.654, R.655, K.658 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.470, B:V.471, B:G.472, B:K.473, B:R.655 Salt bridges: B:R.655, A:R.597 ADP.4: 12 residues within 4Å: Chain C: D.434, H.435, P.469, G.470, V.471, G.472, K.473, T.474, T.583, Y.618, V.654, R.655 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:D.434, C:Y.436, C:G.470, C:V.471, C:G.472, C:T.474, C:T.474, C:T.474, C:D.534 Salt bridges: C:K.473, C:K.473, C:R.655, C:R.655

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J. et al., Cryo-EM structure of hexameric yeast Lon protease (PIM1) highlights the importance of conserved structural elements. J.Biol.Chem. (2022)

Release Date

2022-01-12

Peptides

Lon protease homolog, mitochondrial: ABCDEF
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

endogenous substrate

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