SMTL ID : 8yd2.1

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: 15 residues within 4Å: Chain A: G.54, 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 B: F.117 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:M.85, A:P.111, A:P.111 Hydrogen bonds: A:G.55, A:G.55, A:I.57, A:L.112, A:L.112 BO2.2: 16 residues within 4Å: Chain B: G.50, G.51, G.52, F.53, L.56, S.80, A.81, H.105, Q.106, P.107, S.108, L.109, S.110, I.127, M.130, M.134 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.53, B:L.56, B:P.107 Hydrogen bonds: B:G.51, B:F.53, B:S.108, B:S.108 BO2.3: 15 residues within 4Å: Chain C: G.54, 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 D: F.117 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:M.85, C:P.111, C:P.111 Hydrogen bonds: C:G.55, C:G.55, C:I.57, C:L.112, C:L.112 BO2.4: 16 residues within 4Å: Chain D: G.50, G.51, G.52, F.53, L.56, S.80, A.81, H.105, Q.106, P.107, S.108, L.109, S.110, I.127, M.130, M.134 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.53, D:L.56, D:P.107 Hydrogen bonds: D:G.51, D:F.53, D:S.108, D:S.108 BO2.5: 15 residues within 4Å: Chain E: G.54, 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 F: F.117 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:M.85, E:P.111, E:P.111 Hydrogen bonds: E:G.55, E:G.55, E:I.57, E:L.112, E:L.112 BO2.6: 16 residues within 4Å: Chain F: G.50, G.51, G.52, F.53, L.56, S.80, A.81, H.105, Q.106, P.107, S.108, L.109, S.110, I.127, M.130, M.134 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:F.53, F:L.56 Hydrogen bonds: F:G.51, F:F.53, F:S.108, F:S.108 BO2.7: 15 residues within 4Å: Chain G: G.54, 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 H: F.117 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:M.85, G:P.111, G:P.111 Hydrogen bonds: G:G.55, G:G.55, G:I.57, G:L.112, G:L.112 BO2.8: 16 residues within 4Å: Chain H: G.50, G.51, G.52, F.53, L.56, S.80, A.81, H.105, Q.106, P.107, S.108, L.109, S.110, I.127, M.130, M.134 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:F.53, H:L.56 Hydrogen bonds: H:G.51, H:F.53, H:S.108, H:S.108 BO2.9: 15 residues within 4Å: Chain I: G.54, 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 J: F.117 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:M.85, I:P.111, I:P.111 Hydrogen bonds: I:G.55, I:G.55, I:I.57, I:L.112, I:L.112 BO2.10: 16 residues within 4Å: Chain J: G.50, G.51, G.52, F.53, L.56, S.80, A.81, H.105, Q.106, P.107, S.108, L.109, S.110, I.127, M.130, M.134 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:F.53, J:L.56, J:P.107 Hydrogen bonds: J:G.51, J:F.53, J:S.108, J:S.108 BO2.11: 15 residues within 4Å: Chain K: G.54, 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 L: F.117 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:M.85, K:P.111, K:P.111 Hydrogen bonds: K:G.55, K:G.55, K:I.57, K:L.112, K:L.112 BO2.12: 16 residues within 4Å: Chain L: G.50, G.51, G.52, F.53, L.56, S.80, A.81, H.105, Q.106, P.107, S.108, L.109, S.110, I.127, M.130, M.134 8 PLIP interactions: 8 interactions with chain L Hydrophobic interactions: L:F.53, L:L.56, L:A.81, L:P.107 Hydrogen bonds: L:G.51, L:F.53, L:S.108, L:S.108 BO2.13: 15 residues within 4Å: Chain M: G.54, 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.117 6 PLIP interactions: 6 interactions with chain M Hydrophobic interactions: M:M.85 Hydrogen bonds: M:G.55, M:G.55, M:I.57, M:L.112, M:L.112 BO2.14: 16 residues within 4Å: Chain N: G.50, G.51, G.52, F.53, L.56, S.80, A.81, H.105, Q.106, P.107, S.108, L.109, S.110, I.127, M.130, M.134 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:F.53, N:L.56, N:A.81, N:P.107 Hydrogen bonds: N:G.51, N:F.53, N:S.108, N:S.108

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: ACEGIKM
ATP-dependent Clp protease proteolytic subunit 2: BDFHJLN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

B
B

D
D

F
F

H
H

J
J

L
L

N
N

ATP-dependent Clp protease proteolytic subunit 1

ATP-dependent Clp protease proteolytic subunit 2

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