SMTL ID : 8yd0.1

CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-7-7-mer

Ligands

2 x MG: MAGNESIUM ION

MG.1: 4 residues within 4Å: Chain A: T.69, D.127 Chain B: R.248 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.69 MG.7: 5 residues within 4Å: Chain E: T.64, G.65, K.68 Chain F: E.244 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.244

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.2: 20 residues within 4Å: Chain A: Y.15, V.16, I.17, Q.19, T.64, G.65, C.66, G.67, K.68, T.69, Y.70, Q.128, A.193, L.258, I.266, A.310, R.311 Chain B: E.244, R.248 Ligands: MG.1 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:I.17, A:T.64, A:G.65, A:C.66, A:C.66, A:G.67, A:K.68, A:T.69, A:Y.70, B:E.244, B:E.244, B:E.244 Salt bridges: A:K.68, A:K.68, A:R.311, A:R.311, B:R.248 ATP.3: 21 residues within 4Å: Chain B: Y.15, V.16, I.17, P.63, T.64, G.65, C.66, G.67, K.68, T.69, Y.70, D.127, Q.128, L.258, I.266, P.270, A.310, R.311 Chain C: E.159, E.244, R.248 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:I.17, B:I.17, B:T.64, B:G.65, B:C.66, B:G.67, B:K.68, B:T.69, B:Y.70, B:Q.128, B:Q.128, C:E.159 Salt bridges: B:K.68, B:K.68, B:R.311, B:R.311, C:R.248, C:R.248 ATP.4: 19 residues within 4Å: Chain D: Y.15, V.16, I.17, Q.19, P.63, T.64, G.65, C.66, G.67, K.68, T.69, Y.70, Q.128, I.266, A.310, R.311 Chain E: E.159, E.244, R.248 20 PLIP interactions: 4 interactions with chain E, 16 interactions with chain D Hydrogen bonds: E:E.244, E:E.244, E:E.244, D:I.17, D:T.64, D:G.65, D:C.66, D:C.66, D:G.67, D:K.68, D:T.69, D:T.69, D:Y.70, D:Q.128 Salt bridges: E:R.248, D:K.68, D:K.68, D:R.311, D:R.311, D:R.311 ATP.5: 21 residues within 4Å: Chain C: Y.15, V.16, I.17, Q.19, P.63, T.64, G.65, C.66, G.67, K.68, T.69, Y.70, D.127, Q.128, I.266, P.270, A.310, R.311 Chain D: E.159, E.244, R.248 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.17, C:Q.19, C:T.64, C:G.65, C:C.66, C:C.66, C:G.67, C:K.68, C:T.69, C:T.69, C:Y.70, C:Y.70 Salt bridges: C:K.68, C:K.68, C:R.311, C:R.311, D:R.248

2 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.6: 19 residues within 4Å: Chain E: Y.15, V.16, I.17, G.18, Q.19, T.64, G.65, C.66, G.67, K.68, T.69, Y.70, L.258, I.266, A.310, R.311 Chain F: E.244, R.248 Ligands: MG.7 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:I.17, E:Q.19, E:T.64, E:G.65, E:C.66, E:C.66, E:G.67, E:K.68, E:T.69, E:Y.70, E:Y.70, E:R.311, F:E.244, F:R.248 Salt bridges: E:K.68, E:K.68 ADP.8: 15 residues within 4Å: Chain F: Y.15, V.16, I.17, T.64, G.65, C.66, G.67, K.68, T.69, Y.70, Y.125, L.258, I.266, A.310, R.311 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:I.17, F:G.65, F:C.66, F:C.66, F:G.67, F:K.68, F:T.69, F:Y.70, F:Y.125 Salt bridges: F:K.68, F:R.311, F:R.311

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

BO2.9: 16 residues within 4Å: Chain G: G.66, G.67, G.68, F.69, L.72, S.96, A.97, H.121, Q.122, P.123, S.124, L.125, S.126, I.143, M.146, M.150 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:F.69, G:L.72, G:A.97, G:P.123 Hydrogen bonds: G:F.69, G:S.124, G:S.124 BO2.10: 15 residues within 4Å: Chain H: G.66, G.67, G.68, F.69, L.72, S.96, A.97, H.121, Q.122, P.123, S.124, L.125, S.126, M.146, M.150 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:F.69, H:L.72, H:P.123, H:L.125 Hydrogen bonds: H:G.67, H:G.67, H:G.67, H:F.69, H:A.97, H:S.124, H:S.124 BO2.11: 16 residues within 4Å: Chain I: G.66, G.67, G.68, F.69, L.72, S.96, A.97, H.121, Q.122, P.123, S.124, L.125, S.126, M.146, M.150 Chain T: R.117 10 PLIP interactions: 8 interactions with chain I, 2 interactions with chain T Hydrophobic interactions: I:F.69, I:L.72 Hydrogen bonds: I:G.67, I:G.67, I:F.69, I:A.97, I:S.124, I:S.124, T:R.117, T:R.117 BO2.12: 15 residues within 4Å: Chain J: G.66, G.67, G.68, F.69, L.72, S.96, A.97, H.121, Q.122, P.123, S.124, L.125, S.126, M.146, M.150 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:F.69, J:L.72, J:A.97, J:P.123 Hydrogen bonds: J:F.69, J:S.124, J:S.124 BO2.13: 15 residues within 4Å: Chain K: G.66, G.67, G.68, F.69, L.72, S.96, A.97, H.121, Q.122, P.123, S.124, L.125, S.126, M.146, M.150 7 PLIP interactions: 6 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:F.69, K:L.72, K:P.123 Hydrogen bonds: K:F.69, K:S.124, K:S.124, L:R.117 BO2.14: 16 residues within 4Å: Chain L: G.66, G.67, G.68, F.69, L.72, S.96, A.97, H.121, Q.122, P.123, S.124, L.125, S.126, I.143, M.146, M.150 10 PLIP interactions: 10 interactions with chain L Hydrophobic interactions: L:F.69, L:L.72, L:L.125 Hydrogen bonds: L:G.67, L:G.67, L:G.67, L:F.69, L:A.97, L:S.124, L:S.124 BO2.15: 15 residues within 4Å: Chain J: F.133 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 4 PLIP interactions: 4 interactions with chain M Hydrogen bonds: M:G.55, M:I.57, M:L.112, M:L.112 BO2.16: 15 residues within 4Å: Chain N: 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 T: F.133 4 PLIP interactions: 4 interactions with chain N Hydrogen bonds: N:G.55, N:I.57, N:L.112, N:L.112 BO2.17: 15 residues within 4Å: Chain I: F.133 Chain O: 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 4 PLIP interactions: 4 interactions with chain O Hydrogen bonds: O:G.55, O:I.57, O:L.112, O:L.112 BO2.18: 15 residues within 4Å: Chain G: F.133 Chain P: 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 6 PLIP interactions: 6 interactions with chain P Hydrophobic interactions: P:I.57, P:P.111 Hydrogen bonds: P:G.55, P:I.57, P:L.112, P:L.112 BO2.19: 15 residues within 4Å: Chain K: F.133 Chain Q: 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 4 PLIP interactions: 4 interactions with chain Q Hydrogen bonds: Q:G.55, Q:I.57, Q:L.112, Q:L.112 BO2.20: 15 residues within 4Å: Chain L: F.133 Chain R: 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 4 PLIP interactions: 4 interactions with chain R Hydrogen bonds: R:G.55, R:I.57, R:L.112, R:L.112 BO2.21: 15 residues within 4Å: Chain H: F.133 Chain S: 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 4 PLIP interactions: 4 interactions with chain S Hydrogen bonds: S:G.55, S:I.57, S:L.112, S:L.112 BO2.22: 15 residues within 4Å: Chain T: G.66, G.67, G.68, F.69, L.72, S.96, A.97, H.121, Q.122, P.123, S.124, L.125, S.126, M.146, M.150 11 PLIP interactions: 11 interactions with chain T Hydrophobic interactions: T:F.69, T:L.72, T:A.97, T:L.125 Hydrogen bonds: T:G.67, T:G.67, T:G.67, T:F.69, T:A.97, T:S.124, T:S.124

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 ATP-binding subunit ClpX: ABCDEF
ATP-dependent Clp protease proteolytic subunit 2: GHIJKLT
ATP-dependent Clp protease proteolytic subunit 1: MNOPQRS

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

I
K

J
L

K
M

L
N

T
V

M
O

N
P

O
Q

P
R

Q
S

R
T

S
U

ATP-dependent Clp protease ATP-binding subunit ClpX

ATP-dependent Clp protease proteolytic subunit 2

ATP-dependent Clp protease proteolytic subunit 1

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