SMTL ID : 9jvp.1

CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-7-7-1-mer

Ligands

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.1: 23 residues within 4Å: Chain A: D.21, P.22, V.23, I.24, R.26, E.50, P.51, G.52, V.53, G.54, K.55, T.56, A.57, I.191, L.195, P.229, D.230, I.233 Chain B: R.147, A.170, R.173, R.174 Ligands: MG.3 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.21, A:I.24, A:I.24, A:G.52, A:V.53, A:G.54, A:K.55, A:T.56, A:A.57, B:K.42 Salt bridges: A:K.55, A:K.55, B:R.147, B:R.173, B:R.173, B:R.173, B:R.174 ATP.2: 23 residues within 4Å: Chain A: R.350, I.351, I.352, Q.354, P.387, S.388, G.389, V.390, G.391, K.392, T.393, E.394, N.500, L.555, M.563, L.566, M.567, A.603, R.604, R.607 Chain B: E.476, R.545 Ligands: MG.4 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.352, A:G.389, A:V.390, A:V.390, A:G.391, A:K.392, A:T.393, A:E.394, A:E.394, A:N.500, A:N.500, A:N.500 Salt bridges: A:K.392, A:K.392, A:R.604, A:R.604, A:R.604, B:R.545 ATP.5: 23 residues within 4Å: Chain B: R.350, I.351, I.352, Q.354, P.387, S.388, G.389, V.390, G.391, K.392, T.393, E.394, N.500, M.563, L.566, M.567, A.603, R.604, R.607 Chain C: E.476, E.541, R.545 Ligands: MG.8 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:I.352, B:G.389, B:V.390, B:V.390, B:G.391, B:K.392, B:T.393, B:T.393, B:E.394, B:N.500, C:E.541 Salt bridges: B:K.392, B:K.392, B:R.604, B:R.604, B:R.604, C:R.545 ATP.6: 24 residues within 4Å: Chain B: D.21, P.22, V.23, I.24, R.26, E.50, P.51, G.52, V.53, G.54, K.55, T.56, A.57, T.157, I.191, L.195, Y.199, P.229, D.230, I.233 Chain C: R.147, R.173, R.174 Ligands: MG.7 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:D.21, B:I.24, B:I.24, B:G.52, B:V.53, B:G.54, B:K.55, B:T.56, B:A.57, B:Y.199 Salt bridges: B:K.55, B:K.55, C:R.147, C:R.173, C:R.173, C:R.173, C:R.174 ATP.9: 23 residues within 4Å: Chain C: R.350, I.351, I.352, Q.354, P.387, S.388, G.389, V.390, G.391, K.392, T.393, E.394, L.555, M.563, L.566, M.567, A.603, R.604, R.607 Chain D: E.476, E.541, R.545 Ligands: MG.12 21 PLIP interactions: 16 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:I.352, C:G.389, C:V.390, C:V.390, C:G.391, C:K.392, C:T.393, C:T.393, C:E.394, C:E.394, C:R.607, D:E.476, D:E.476, D:E.541, D:E.541 Salt bridges: C:K.392, C:K.392, C:R.604, C:R.604, C:R.604, D:R.545 ATP.10: 23 residues within 4Å: Chain C: D.21, P.22, V.23, I.24, R.26, P.51, G.52, V.53, G.54, K.55, T.56, A.57, T.157, I.191, L.195, P.229, I.233 Chain D: T.41, R.147, A.170, R.173, R.174 Ligands: MG.11 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:I.24, C:I.24, C:G.52, C:G.54, C:K.55, C:T.56, C:A.57, D:R.147 Salt bridges: C:K.55, C:K.55, D:R.147, D:R.173, D:R.173, D:R.173, D:R.174 ATP.13: 25 residues within 4Å: Chain D: D.21, P.22, V.23, I.24, R.26, E.50, P.51, G.52, V.53, G.54, K.55, T.56, A.57, T.157, I.191, L.195, Y.199, P.229, D.230, I.233 Chain E: R.147, A.170, R.173, R.174 Ligands: MG.16 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:D.21, D:I.24, D:I.24, D:G.52, D:V.53, D:G.54, D:K.55, D:T.56, D:T.56, D:A.57, D:T.157, D:Y.199 Salt bridges: D:K.55, D:K.55, E:R.147, E:R.173, E:R.173, E:R.173, E:R.174 ATP.14: 18 residues within 4Å: Chain D: R.350, I.351, I.352, S.388, G.389, V.390, G.391, K.392, T.393, E.394, N.500, L.555, M.563, M.567, A.603, R.604, R.607 Ligands: MG.15 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:I.352, D:G.389, D:V.390, D:V.390, D:G.391, D:K.392, D:T.393, D:E.394, D:E.394, D:N.500, D:N.500, D:R.607 Salt bridges: D:K.392, D:K.392, D:R.604, D:R.604, D:R.604

8 x MG: MAGNESIUM ION

MG.3: 4 residues within 4Å: Chain A: T.56, D.120 Chain B: R.174 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.56 MG.4: 4 residues within 4Å: Chain A: T.393, D.458 Chain B: R.545 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.393 MG.7: 3 residues within 4Å: Chain B: T.56, D.120 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.56 MG.8: 4 residues within 4Å: Chain B: T.393, D.458 Chain C: R.545 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.393 MG.11: 3 residues within 4Å: Chain C: T.56, D.120 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.56 MG.12: 4 residues within 4Å: Chain C: T.393, D.458 Chain D: R.545 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.393 MG.15: 4 residues within 4Å: Chain D: K.392, T.393, D.458 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.393 MG.16: 4 residues within 4Å: Chain D: T.56, D.120 Chain E: R.174 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.56

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.17: 21 residues within 4Å: Chain E: D.21, P.22, V.23, I.24, G.25, R.26, E.50, P.51, G.52, V.53, G.54, K.55, T.56, A.57, H.187, I.191, L.195, P.229, D.230, I.233 Chain F: R.173 13 PLIP interactions: 2 interactions with chain F, 11 interactions with chain E Hydrogen bonds: F:R.173, E:I.24, E:I.24, E:G.52, E:V.53, E:G.54, E:K.55, E:T.56, E:T.56, E:T.56, E:A.57 Salt bridges: F:R.173, E:K.55 ADP.18: 19 residues within 4Å: Chain E: R.350, I.351, I.352, G.353, Q.354, P.387, S.388, G.389, V.390, G.391, K.392, T.393, E.394, M.563, M.567, R.570, A.603, R.604, R.607 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:I.352, E:G.353, E:S.388, E:G.389, E:V.390, E:G.391, E:K.392, E:T.393, E:E.394, E:E.394, E:R.607 Salt bridges: E:R.604, E:R.604 ADP.19: 15 residues within 4Å: Chain F: R.350, I.351, I.352, G.353, Q.354, K.392, T.393, E.394, L.501, M.563, L.566, M.567, A.603, R.604, R.607 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:I.352, F:I.352, F:K.392, F:T.393, F:T.393 Salt bridges: F:K.397, F:R.604, F:R.604 ADP.20: 20 residues within 4Å: Chain A: R.173 Chain F: P.22, V.23, I.24, G.25, R.26, E.50, P.51, G.52, V.53, G.54, K.55, T.56, A.57, E.60, I.191, L.195, P.229, D.230, I.233 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:I.24, F:R.26, F:E.50, F:G.52, F:V.53, F:G.54, F:K.55, F:T.56, F:A.57 Salt bridges: F:K.55, A:R.173, A:R.173

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

BO2.21: 14 residues within 4Å: Chain G: G.51, G.52, F.53, L.56, S.80, A.81, H.105, Q.106, P.107, S.108, L.109, S.110, M.130, M.134 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:F.53, G:L.56, G:A.81, G:P.107 Hydrogen bonds: G:G.51, G:G.52, G:F.53, G:Q.106, G:S.108, G:S.108 BO2.22: 15 residues within 4Å: Chain H: G.51, G.52, F.53, L.56, S.80, A.81, V.84, H.105, Q.106, P.107, S.108, L.109, S.110, M.130, M.134 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:F.53, H:L.56, H:A.81, H:V.84, H:P.107, H:M.134 Hydrogen bonds: H:G.52, H:G.52, H:F.53, H:Q.106, H:S.108 BO2.23: 13 residues within 4Å: Chain I: G.51, G.52, F.53, L.56, S.80, A.81, H.105, P.107, S.108, L.109, S.110, M.130, M.134 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:F.53, I:L.56, I:P.107, I:M.134 Hydrogen bonds: I:G.51, I:G.52, I:F.53, I:S.108, I:S.108 BO2.24: 14 residues within 4Å: Chain J: G.50, G.51, G.52, F.53, L.56, S.80, A.81, H.105, P.107, S.108, L.109, S.110, M.130, M.134 10 PLIP interactions: 10 interactions with chain J Hydrophobic interactions: J:F.53, J:L.56, J:A.81, J:P.107, J:M.134 Hydrogen bonds: J:G.51, J:F.53, J:A.81, J:S.108, J:S.108 BO2.25: 16 residues within 4Å: Chain K: Q.17, G.50, G.51, G.52, F.53, L.56, S.80, A.81, H.105, P.107, S.108, L.109, S.110, I.127, M.130, M.134 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:F.53, K:L.56, K:A.81, K:P.107, K:M.134 Hydrogen bonds: K:G.51, K:G.52, K:G.52, K:F.53, K:A.81, K:S.108 BO2.26: 15 residues within 4Å: Chain L: G.51, G.52, F.53, L.56, S.80, A.81, V.84, H.105, Q.106, P.107, S.108, L.109, S.110, M.130, M.134 10 PLIP interactions: 10 interactions with chain L Hydrophobic interactions: L:F.53, L:V.84, L:P.107 Hydrogen bonds: L:G.51, L:G.51, L:G.52, L:F.53, L:A.81, L:S.108, L:S.108 BO2.27: 15 residues within 4Å: Chain M: G.50, G.51, G.52, F.53, L.56, S.80, A.81, H.105, P.107, S.108, L.109, S.110, I.127, M.130, M.134 11 PLIP interactions: 11 interactions with chain M Hydrophobic interactions: M:F.53, M:L.56, M:A.81, M:P.107, M:M.134 Hydrogen bonds: M:G.51, M:G.52, M:G.52, M:F.53, M:A.81, M:S.108 BO2.28: 15 residues within 4Å: Chain G: F.117 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 7 PLIP interactions: 7 interactions with chain N Hydrophobic interactions: N:I.57 Hydrogen bonds: N:G.55, N:G.55, N:I.57, N:M.85, N:L.112, N:L.112 BO2.29: 15 residues within 4Å: Chain H: F.117 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 8 PLIP interactions: 8 interactions with chain O Hydrophobic interactions: O:I.57, O:M.85, O:P.111 Hydrogen bonds: O:G.55, O:G.55, O:I.57, O:M.85, O:L.112 BO2.30: 15 residues within 4Å: Chain I: F.117 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 9 PLIP interactions: 9 interactions with chain P Hydrophobic interactions: P:I.57, P:P.111 Hydrogen bonds: P:G.55, P:G.55, P:G.55, P:I.57, P:M.85, P:L.112, P:L.112 BO2.31: 15 residues within 4Å: Chain J: F.117 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 10 PLIP interactions: 10 interactions with chain Q Hydrophobic interactions: Q:I.57, Q:P.111 Hydrogen bonds: Q:G.55, Q:G.55, Q:G.55, Q:G.55, Q:I.57, Q:M.85, Q:L.112, Q:L.112 BO2.32: 15 residues within 4Å: Chain K: F.117 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 9 PLIP interactions: 9 interactions with chain R Hydrophobic interactions: R:I.57, R:P.111, R:P.111 Hydrogen bonds: R:G.55, R:G.55, R:G.55, R:I.57, R:M.85, R:L.112 BO2.33: 15 residues within 4Å: Chain L: F.117 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 9 PLIP interactions: 9 interactions with chain S Hydrophobic interactions: S:I.57, S:P.111 Hydrogen bonds: S:G.55, S:G.55, S:G.55, S:I.57, S:M.85, S:L.112, S:L.112 BO2.34: 15 residues within 4Å: Chain M: F.117 Chain T: 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 8 PLIP interactions: 8 interactions with chain T Hydrophobic interactions: T:I.57, T:M.85, T:P.111 Hydrogen bonds: T:G.55, T:G.55, T:I.57, T:M.85, T:L.112

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 ClpC1: ABCDEF
ATP-dependent Clp protease proteolytic subunit 2: GHIJKLM
ATP-dependent Clp protease proteolytic subunit 1: NOPQRST
Beta-casein: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
M

H
G

I
H

J
I

K
J

L
K

M
L

N
T

O
N

P
O

Q
P

R
Q

S
R

T
S

U
U

ATP-dependent Clp protease ATP-binding subunit ClpC1

ATP-dependent Clp protease proteolytic subunit 2

ATP-dependent Clp protease proteolytic subunit 1

Beta-casein

Related Entries With Identical Sequence