SMTL ID : 9dw3.1

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: 13 residues within 4Å: Chain A: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.68, A:P.123, A:L.148 Hydrogen bonds: A:G.67, A:G.67, A:G.67, A:V.69, A:M.97, A:S.124, A:S.124 BO2.2: 13 residues within 4Å: Chain B: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.68, B:P.123, B:L.148 Hydrogen bonds: B:G.67, B:G.67, B:G.67, B:V.69, B:M.97, B:S.124, B:S.124 BO2.3: 13 residues within 4Å: Chain C: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.68, C:P.123, C:L.148 Hydrogen bonds: C:G.67, C:G.67, C:G.67, C:V.69, C:M.97, C:S.124, C:S.124 BO2.4: 13 residues within 4Å: Chain D: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:V.68, D:P.123, D:L.148 Hydrogen bonds: D:G.67, D:G.67, D:G.67, D:V.69, D:M.97, D:S.124, D:S.124 BO2.5: 13 residues within 4Å: Chain E: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:V.68, E:P.123, E:L.148 Hydrogen bonds: E:G.67, E:G.67, E:G.67, E:V.69, E:M.97, E:S.124, E:S.124 BO2.6: 13 residues within 4Å: Chain F: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:V.68, F:P.123, F:L.148 Hydrogen bonds: F:G.67, F:G.67, F:G.67, F:V.69, F:M.97, F:S.124, F:S.124 BO2.7: 13 residues within 4Å: Chain G: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:V.68, G:P.123, G:L.148 Hydrogen bonds: G:G.67, G:G.67, G:G.67, G:V.69, G:M.97, G:S.124, G:S.124 BO2.8: 13 residues within 4Å: Chain H: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:V.68, H:P.123, H:L.148 Hydrogen bonds: H:G.67, H:G.67, H:G.67, H:V.69, H:M.97, H:S.124, H:S.124 BO2.9: 13 residues within 4Å: Chain I: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:V.68, I:P.123, I:L.148 Hydrogen bonds: I:G.67, I:G.67, I:G.67, I:V.69, I:M.97, I:S.124, I:S.124 BO2.10: 13 residues within 4Å: Chain J: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain J Hydrophobic interactions: J:V.68, J:P.123, J:L.148 Hydrogen bonds: J:G.67, J:G.67, J:G.67, J:V.69, J:M.97, J:S.124, J:S.124 BO2.11: 13 residues within 4Å: Chain K: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:V.68, K:P.123, K:L.148 Hydrogen bonds: K:G.67, K:G.67, K:G.67, K:V.69, K:M.97, K:S.124, K:S.124 BO2.12: 13 residues within 4Å: Chain L: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain L Hydrophobic interactions: L:V.68, L:P.123, L:L.148 Hydrogen bonds: L:G.67, L:G.67, L:G.67, L:V.69, L:M.97, L:S.124, L:S.124 BO2.13: 13 residues within 4Å: Chain M: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain M Hydrophobic interactions: M:V.68, M:P.123, M:L.148 Hydrogen bonds: M:G.67, M:G.67, M:G.67, M:V.69, M:M.97, M:S.124, M:S.124 BO2.14: 13 residues within 4Å: Chain N: G.66, G.67, V.68, V.69, S.96, M.97, H.121, Q.122, P.123, S.124, I.141, L.144, L.148 10 PLIP interactions: 10 interactions with chain N Hydrophobic interactions: N:V.68, N:P.123, N:L.148 Hydrogen bonds: N:G.67, N:G.67, N:G.67, N:V.69, N:M.97, N:S.124, N:S.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, W.C., Assembly and proteolytic activation human ClpXP defined by cryo-EM. To Be Published

Release Date

2025-10-15

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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