SMTL ID : 7krz.1

Human mitochondrial LONP1 in complex with Bortezomib

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: H.78, Y.79, M.81, P.112, G.113, V.114, G.115, K.116, T.117, S.118, Y.248, I.256, Y.260, V.296, R.297 Chain B: E.201, R.239 Ligands: MG.2 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.79, A:G.113, A:V.114, A:G.115, A:K.116, A:T.117, A:S.118, A:S.118, A:S.118, A:Y.248 Salt bridges: A:K.116, A:K.116, A:R.297, A:R.297, A:R.297, B:R.239 pi-Cation interactions: A:H.78 ATP.4: 20 residues within 4Å: Chain B: H.78, Y.79, M.81, P.111, P.112, G.113, V.114, G.115, K.116, T.117, S.118, E.178, Y.248, I.256, Y.260, V.296, R.297 Chain C: E.201, R.239 Ligands: MG.5 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.79, B:G.113, B:V.114, B:G.115, B:K.116, B:T.117, B:S.118, B:Y.248 Salt bridges: B:K.116, B:K.116, B:R.297, B:R.297, B:R.297, C:R.239 pi-Cation interactions: B:H.78 ATP.7: 19 residues within 4Å: Chain C: D.77, H.78, Y.79, P.112, G.113, V.114, G.115, K.116, T.117, S.118, N.227, Y.248, I.256, Y.260, V.296, R.297 Chain D: E.201, R.239 Ligands: MG.8 21 PLIP interactions: 19 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.79, C:G.113, C:V.114, C:G.115, C:K.116, C:T.117, C:S.118, C:S.118, C:S.118, C:N.227, C:N.227, C:Y.248, D:E.201 Salt bridges: C:K.116, C:K.116, C:R.297, C:R.297, C:R.297, D:R.239 pi-Stacking: C:H.78, C:H.78 ATP.10: 20 residues within 4Å: Chain D: D.77, H.78, Y.79, M.81, P.111, P.112, G.113, V.114, G.115, K.116, T.117, S.118, N.227, Y.248, I.256, Y.260, V.296, R.297, Q.300 Ligands: MG.11 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Y.79, D:G.113, D:V.114, D:G.115, D:K.116, D:T.117, D:T.117, D:S.118, D:Y.248, D:Q.300 Salt bridges: D:K.116, D:K.116, D:R.297, D:R.297, D:R.297 pi-Cation interactions: D:H.78

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.117, D.177, E.178 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.117 MG.5: 4 residues within 4Å: Chain B: T.117, D.177, E.178 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.117 MG.8: 3 residues within 4Å: Chain C: T.117, D.177 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.117 MG.11: 3 residues within 4Å: Chain D: T.117, D.177 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.117

6 x BO2: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE(Non-covalent)(Covalent)

BO2.3: 15 residues within 4Å: Chain A: L.355, A.356, W.357, T.358, L.365, M.397, T.436, P.437, K.438, D.439, G.440, P.441, S.442, A.443, K.485 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.357, A:L.365, A:A.443 Hydrogen bonds: A:W.357, A:W.357, A:T.436, A:D.439, A:D.439, A:S.442, A:K.485 BO2.6: 14 residues within 4Å: Chain B: L.355, A.356, W.357, T.358, L.365, M.397, T.436, K.438, D.439, G.440, P.441, S.442, A.443, K.485 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.357, B:L.365, B:A.443 Hydrogen bonds: B:W.357, B:W.357, B:D.439, B:D.439, B:S.442, B:K.485 BO2.9: 13 residues within 4Å: Chain C: L.355, A.356, W.357, T.358, L.365, M.397, K.438, D.439, G.440, P.441, S.442, A.443, K.485 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.365, C:L.365, C:A.443 Hydrogen bonds: C:W.357, C:W.357, C:D.439, C:D.439, C:S.442, C:K.485 BO2.12: 16 residues within 4Å: Chain D: L.355, A.356, W.357, T.358, S.363, L.365, M.397, T.436, P.437, K.438, D.439, G.440, P.441, S.442, A.443, K.485 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:A.356, D:W.357, D:L.365, D:A.443 Hydrogen bonds: D:W.357, D:W.357, D:D.439, D:D.439, D:D.439, D:S.442, D:K.485 BO2.14: 14 residues within 4Å: Chain E: A.356, W.357, T.358, L.365, M.397, T.436, P.437, K.438, D.439, G.440, P.441, S.442, A.443, K.485 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:A.356, E:L.365, E:A.443 Hydrogen bonds: E:W.357, E:W.357, E:T.436, E:D.439, E:D.439, E:S.442, E:K.485 BO2.16: 13 residues within 4Å: Chain F: L.355, A.356, W.357, T.358, M.397, T.436, K.438, D.439, G.440, P.441, S.442, A.443, K.485 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:A.443 Hydrogen bonds: F:W.357, F:W.357, F:D.439, F:D.439, F:S.442, F:K.485

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

ADP.13: 15 residues within 4Å: Chain E: H.78, Y.79, P.112, G.113, V.114, G.115, K.116, T.117, S.118, N.227, Y.248, I.256, Y.260, V.296, Q.300 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:Y.79, E:G.113, E:V.114, E:G.115, E:K.116, E:T.117, E:T.117, E:T.117, E:N.227, E:Y.248, E:Q.264, E:Q.300 Salt bridges: E:K.116, E:K.116 pi-Stacking: E:Y.260 pi-Cation interactions: E:H.78 ADP.15: 13 residues within 4Å: Chain F: H.78, Y.79, G.113, V.114, G.115, K.116, T.117, S.118, Y.248, I.256, Y.260, V.296, Q.300 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:H.78, F:Y.79, F:G.113, F:V.114, F:G.115, F:K.116, F:T.117, F:T.117, F:T.117, F:Y.248 Salt bridges: F:K.116 pi-Stacking: F:Y.260 pi-Cation interactions: F:H.78

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

2021-02-24

Peptides

Lon protease homolog, mitochondrial: ABCDEF
Endogenous co-purified 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 co-purified substrate

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