SMTL ID : 6on2.1

Lon Protease from Yersinia pestis with Y2853 substrate

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

1 x ALA- ALA- ALA- ALA- ALA- ALA- ALA: Bound Y2853 Substrate(Non-covalent)

ALA-ALA-ALA-ALA-ALA-ALA-ALA.1: 13 residues within 4Å: Chain A: T.145, Y.146, I.147 Chain B: T.145, Y.146, I.147, R.181 Chain C: T.145, Y.146, I.147 Chain D: Y.146, I.147 Chain F: I.147 9 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F, 2 interactions with chain C, 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:Y.146, B:I.147, F:I.147, C:Y.146, A:Y.146 Salt bridges: B:R.181 Hydrogen bonds: C:I.147, A:I.147, D:I.147

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

ATP.2: 21 residues within 4Å: Chain A: D.71, H.72, Y.73, P.105, P.106, G.107, V.108, G.109, K.110, T.111, S.112, N.221, Y.241, I.249, H.253, K.257, V.289, R.290 Chain B: E.195, R.232 Ligands: MG.3 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.73, A:G.107, A:V.108, A:G.109, A:K.110, A:T.111, A:T.111, A:S.112, A:N.221, A:Y.241, A:K.257, B:E.195 Salt bridges: A:K.110, A:K.110, A:R.290, A:R.290, A:R.290, B:R.232 pi-Stacking: A:H.72 pi-Cation interactions: A:H.72 ATP.4: 19 residues within 4Å: Chain B: H.72, Y.73, P.106, G.107, V.108, G.109, K.110, T.111, S.112, N.221, Y.241, I.249, H.253, K.257, V.289, R.290 Chain C: E.195, R.232 Ligands: MG.5 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.73, B:G.107, B:V.108, B:G.109, B:K.110, B:T.111, B:S.112, B:S.112, B:Q.172, B:N.221, B:Y.241, B:Y.241, B:K.257, C:E.195 Salt bridges: B:K.110, B:K.110, B:R.290, B:R.290, B:R.290, C:R.232 pi-Stacking: B:H.72 ATP.6: 22 residues within 4Å: Chain C: D.71, H.72, Y.73, P.106, G.107, V.108, G.109, K.110, T.111, S.112, Q.172, N.221, Y.241, I.249, H.253, K.257, V.289, R.290 Chain D: D.193, E.195, R.232 Ligands: MG.7 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.73, C:G.107, C:V.108, C:G.109, C:K.110, C:T.111, C:S.112, C:Q.172, C:N.221, C:Y.241, C:Y.241, C:K.257, D:D.193 Salt bridges: C:K.110, C:K.110, C:R.290, C:R.290, C:R.290, D:R.232 pi-Stacking: C:H.72 ATP.8: 19 residues within 4Å: Chain D: H.72, Y.73, P.105, P.106, G.107, V.108, G.109, K.110, T.111, S.112, N.221, Y.241, I.249, H.253, K.257, V.289, R.290, E.293 Ligands: MG.9 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:Y.73, D:G.107, D:V.108, D:G.109, D:K.110, D:T.111, D:T.111, D:S.112, D:S.112, D:S.112, D:N.221, D:N.221, D:Y.241, D:K.257, D:E.293 Salt bridges: D:K.110, D:K.110, D:R.290, D:R.290, D:R.290 pi-Stacking: D:H.72

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.111 Chain B: R.232 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.111 MG.5: 3 residues within 4Å: Chain B: T.111 Chain C: R.232 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.111 MG.7: 4 residues within 4Å: Chain C: T.111 Chain D: D.193, R.232 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.111 MG.9: 3 residues within 4Å: Chain D: T.111, D.171 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.111 MG.11: 3 residues within 4Å: Chain E: T.111, D.171 Ligands: ADP.10 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.111, E:D.171

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

ADP.10: 15 residues within 4Å: Chain E: D.71, H.72, Y.73, L.75, P.106, G.107, V.108, G.109, K.110, T.111, Y.241, I.249, V.289, R.290 Ligands: MG.11 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:Y.73, E:Y.73, E:G.107, E:K.110, E:T.111, E:T.111 Salt bridges: E:K.110, E:R.290, E:R.290 pi-Stacking: E:H.72 ADP.12: 16 residues within 4Å: Chain F: D.71, H.72, Y.73, P.106, G.107, V.108, G.109, K.110, T.111, Q.172, Y.241, I.249, H.253, K.257, V.289, R.290 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Y.73, F:G.74, F:G.107, F:G.109, F:K.110, F:T.111, F:T.111, F:T.111, F:Q.172, F:Y.241 Salt bridges: F:K.110, F:R.290, F:R.290 pi-Stacking: F:H.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, M. et al., Structural basis for distinct operational modes and protease activation in AAA+ protease Lon. Sci Adv (2020)

Release Date

2019-05-01

Peptides

ATP-dependent protease La: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ATP-dependent protease La