SMTL ID : 9jvz.1

CryoEM structure of M. tuberculosis ClpP1P2 bound to bortezomib

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-7-mer

Ligands

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

BO2.1: 14 residues within 4Å: Chain A: G.54, G.55, S.56, I.57, S.84, M.85, H.109, P.111, L.112, G.113, F.129, I.132, M.136 Chain L: F.132 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.111, A:P.111 Hydrogen bonds: A:G.55, A:G.55, A:I.57, A:M.85, A:L.112, A:L.112 BO2.2: 15 residues within 4Å: Chain B: E.21, G.54, G.55, S.56, I.57, S.84, M.85, H.109, P.111, L.112, G.113, F.129, I.132, M.136 Chain M: F.132 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.57, B:P.111 Hydrogen bonds: B:G.55, B:G.55, B:I.57, B:L.112 BO2.3: 14 residues within 4Å: Chain C: G.54, G.55, S.56, I.57, S.84, M.85, H.109, P.111, L.112, G.113, F.129, I.132, M.136 Chain J: F.132 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:P.111 Hydrogen bonds: C:G.55, C:G.55, C:G.55, C:I.57, C:M.85, C:L.112, C:L.112 BO2.4: 15 residues within 4Å: Chain D: E.21, G.54, G.55, S.56, I.57, S.84, M.85, H.109, P.111, L.112, G.113, F.129, I.132, M.136 Chain I: F.132 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.57, D:P.111 Hydrogen bonds: D:G.55, D:G.55, D:I.57, D:L.112, D:L.112 BO2.5: 14 residues within 4Å: Chain E: G.54, G.55, S.56, I.57, S.84, M.85, H.109, P.111, L.112, G.113, F.129, I.132, M.136 Chain G: F.132 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:I.57, E:P.111 Hydrogen bonds: E:G.55, E:G.55, E:I.57, E:L.112, E:L.112 BO2.6: 14 residues within 4Å: Chain F: G.55, S.56, I.57, S.84, M.85, H.109, Q.110, P.111, L.112, G.113, F.129, I.132, M.136 Chain N: F.132 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:P.111 Hydrogen bonds: F:G.55, F:I.57, F:L.112, F:L.112 BO2.7: 16 residues within 4Å: Chain G: Q.32, G.66, G.67, F.68, L.71, S.95, A.96, H.120, Q.121, P.122, S.123, L.124, S.125, I.142, M.145, M.149 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:F.68, G:L.71, G:M.149 Hydrogen bonds: G:G.66, G:G.66, G:F.68, G:S.123 BO2.8: 15 residues within 4Å: Chain H: G.54, G.55, S.56, I.57, S.84, M.85, F.88, H.109, P.111, L.112, G.113, F.129, I.132, M.136 Chain K: F.132 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:F.88, H:P.111 Hydrogen bonds: H:G.55, H:I.57, H:M.85, H:L.112, H:L.112 BO2.9: 15 residues within 4Å: Chain I: Q.32, G.66, G.67, F.68, L.71, S.95, A.96, H.120, Q.121, P.122, S.123, L.124, I.142, M.145, M.149 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:F.68, I:L.71, I:A.96 Hydrogen bonds: I:G.66, I:G.66, I:F.68, I:S.123, I:S.123 BO2.10: 16 residues within 4Å: Chain J: Q.32, G.66, G.67, F.68, L.71, S.95, A.96, H.120, Q.121, P.122, S.123, L.124, S.125, I.142, M.145, M.149 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:F.68, J:L.71, J:A.96 Hydrogen bonds: J:G.66, J:G.66, J:F.68, J:S.123 BO2.11: 16 residues within 4Å: Chain K: Q.32, G.66, G.67, F.68, L.71, S.95, A.96, H.120, Q.121, P.122, S.123, L.124, S.125, I.142, M.145, M.149 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:F.68, K:L.71 Hydrogen bonds: K:G.66, K:G.66, K:F.68, K:S.123 BO2.12: 16 residues within 4Å: Chain L: Q.32, G.66, G.67, F.68, L.71, S.95, A.96, H.120, Q.121, P.122, S.123, L.124, S.125, I.142, M.145, M.149 7 PLIP interactions: 1 interactions with chain K, 6 interactions with chain L Hydrogen bonds: K:R.116, L:G.66, L:G.66, L:F.68, L:S.123 Hydrophobic interactions: L:F.68, L:L.71 BO2.13: 17 residues within 4Å: Chain M: Q.32, G.66, G.67, F.68, L.71, S.95, A.96, V.99, H.120, Q.121, P.122, S.123, L.124, S.125, I.142, M.145, M.149 8 PLIP interactions: 1 interactions with chain L, 7 interactions with chain M Hydrogen bonds: L:R.116, M:G.66, M:G.66, M:F.68, M:S.123 Hydrophobic interactions: M:L.71, M:V.99, M:P.122 BO2.14: 16 residues within 4Å: Chain N: G.65, G.66, G.67, F.68, L.71, S.95, A.96, H.120, Q.121, P.122, S.123, L.124, S.125, I.142, M.145, M.149 12 PLIP interactions: 12 interactions with chain N Hydrophobic interactions: N:F.68, N:L.71, N:A.96, N:M.149 Hydrogen bonds: N:G.66, N:G.66, N:G.66, N:G.66, N:F.68, N:A.96, N:S.123, N:S.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, B. et al., Activation mechanism of caseinolytic chaperone-protease system in Mycobacterium tuberculosis by the anti-cancer drug bortezomib. To Be Published

Release Date

2025-03-19

Peptides

ATP-dependent Clp protease proteolytic subunit 1: ABCDEFH
ATP-dependent Clp protease proteolytic subunit 2: GIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

H
H

G
G

I
I

J
J

K
K

L
L

M
M

N
N

ATP-dependent Clp protease proteolytic subunit 1

ATP-dependent Clp protease proteolytic subunit 2

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