SMTL ID : 9dkw.1

Human mitochondrial ClpP in complex with Bortezomib

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

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

BO2.1: 11 residues within 4Å: Chain A: G.67, G.68, V.69, V.70, S.97, M.98, H.122, Q.123, P.124, S.125, I.142 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.69, A:P.124 Hydrogen bonds: A:G.68, A:G.68, A:G.68, A:V.70, A:M.98, A:S.125, A:S.125 BO2.2: 9 residues within 4Å: Chain B: G.67, G.68, V.69, V.70, S.97, H.122, Q.123, P.124, S.125 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.69, B:P.124 Hydrogen bonds: B:G.68, B:G.68, B:G.68, B:V.70, B:S.125, B:S.125 Water bridges: B:H.122 BO2.3: 10 residues within 4Å: Chain C: G.67, G.68, V.69, V.70, S.97, H.122, Q.123, P.124, S.125, I.142 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.69, C:P.124 Hydrogen bonds: C:G.68, C:G.68, C:G.68, C:V.70, C:S.125, C:S.125 Water bridges: C:H.122 BO2.4: 10 residues within 4Å: Chain D: G.67, G.68, V.69, V.70, S.97, H.122, Q.123, P.124, S.125, I.142 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.69, D:P.124 Hydrogen bonds: D:G.68, D:G.68, D:G.68, D:V.70, D:S.125, D:S.125 Water bridges: D:H.122 BO2.5: 10 residues within 4Å: Chain E: G.67, G.68, V.69, V.70, S.97, M.98, H.122, Q.123, P.124, S.125 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:V.69, E:P.124 Hydrogen bonds: E:G.68, E:G.68, E:G.68, E:V.70, E:M.98, E:S.125, E:S.125 BO2.6: 10 residues within 4Å: Chain F: G.67, G.68, V.69, V.70, S.97, H.122, Q.123, P.124, S.125, I.142 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:V.69, F:P.124 Hydrogen bonds: F:G.68, F:G.68, F:G.68, F:V.70, F:S.125, F:S.125 Water bridges: F:H.122 BO2.7: 11 residues within 4Å: Chain G: G.67, G.68, V.69, V.70, S.97, M.98, H.122, Q.123, P.124, S.125, I.142 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:V.69, G:P.124 Hydrogen bonds: G:G.68, G:G.68, G:G.68, G:V.70, G:M.98, G:S.125, G:S.125 BO2.8: 11 residues within 4Å: Chain H: G.67, G.68, V.69, V.70, S.97, M.98, H.122, Q.123, P.124, S.125, I.142 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:V.69, H:P.124 Hydrogen bonds: H:G.68, H:G.68, H:G.68, H:V.70, H:M.98, H:S.125, H:S.125 BO2.9: 10 residues within 4Å: Chain I: G.67, G.68, V.69, V.70, S.97, H.122, Q.123, P.124, S.125, I.142 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:V.69, I:P.124 Hydrogen bonds: I:G.68, I:G.68, I:G.68, I:V.70, I:S.125, I:S.125 Water bridges: I:H.122 BO2.10: 11 residues within 4Å: Chain J: G.67, G.68, V.69, V.70, S.97, M.98, H.122, Q.123, P.124, S.125, I.142 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:V.69, J:P.124 Hydrogen bonds: J:G.68, J:G.68, J:G.68, J:V.70, J:M.98, J:S.125, J:S.125 BO2.11: 11 residues within 4Å: Chain K: G.67, G.68, V.69, V.70, S.97, M.98, H.122, Q.123, P.124, S.125, I.142 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:V.69, K:P.124 Hydrogen bonds: K:G.68, K:G.68, K:G.68, K:V.70, K:M.98, K:S.125, K:S.125 BO2.12: 11 residues within 4Å: Chain L: G.67, G.68, V.69, V.70, S.97, M.98, H.122, Q.123, P.124, S.125, I.142 9 PLIP interactions: 9 interactions with chain L Hydrophobic interactions: L:V.69, L:P.124 Hydrogen bonds: L:G.68, L:G.68, L:G.68, L:V.70, L:M.98, L:S.125, L:S.125 BO2.13: 12 residues within 4Å: Chain M: G.67, G.68, V.69, V.70, S.97, M.98, H.122, Q.123, P.124, S.125, I.142, L.149 10 PLIP interactions: 10 interactions with chain M Hydrophobic interactions: M:V.69, M:P.124, M:L.149 Hydrogen bonds: M:G.68, M:G.68, M:G.68, M:V.70, M:M.98, M:S.125, M:S.125 BO2.14: 11 residues within 4Å: Chain N: G.67, G.68, V.69, V.70, S.97, M.98, H.122, Q.123, P.124, S.125, I.142 9 PLIP interactions: 9 interactions with chain N Hydrophobic interactions: N:V.69, N:P.124 Hydrogen bonds: N:G.68, N:G.68, N:G.68, N:V.70, N:M.98, N:S.125, N:S.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goncalves, M.M. et al., Mechanism of allosteric activation in human mitochondrial ClpP protease. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-04-23

Peptides

ATP-dependent Clp protease proteolytic subunit, mitochondrial: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

ATP-dependent Clp protease proteolytic subunit, mitochondrial

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