SMTL ID : 8yd1.1

CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-7-7-1-mer

Ligands

7 x MG: MAGNESIUM ION

MG.1: 2 residues within 4Å: Chain A: T.56 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.56 MG.3: 4 residues within 4Å: Chain A: T.393, D.458 Chain B: R.545 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: T.56, D.120 Chain C: R.174 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.56 MG.6: 6 residues within 4Å: Chain B: K.392, T.393, D.458, R.604 Chain C: R.545 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.393 MG.10: 4 residues within 4Å: Chain C: T.56 Chain D: R.173, R.174 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.11: 6 residues within 4Å: Chain C: K.392, T.393, D.458, N.500 Chain D: R.545 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.393 MG.14: 4 residues within 4Å: Chain D: K.55, T.56 Chain E: R.174 Ligands: ATP.15 No protein-ligand interaction detected (PLIP)

7 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.2: 21 residues within 4Å: Chain A: R.350, I.351, I.352, P.387, 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 Chain B: E.476, R.545 Ligands: MG.3 18 PLIP interactions: 2 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:E.476, A:R.350, A:I.352, A:G.389, A:V.390, A:G.391, A:G.391, A:K.392, A:T.393, A:E.394, A:N.500, A:R.607 Salt bridges: B:R.545, A:K.392, A:K.392, A:R.604, A:R.604, A:R.604 ATP.4: 21 residues within 4Å: Chain A: D.21, P.22, V.23, I.24, R.26, P.51, G.52, V.53, G.54, K.55, T.56, A.57, E.60, I.191, P.229, D.230, I.233 Chain B: T.41, R.173, R.174 Ligands: MG.1 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:I.24, A:R.26, A:G.52, A:G.54, A:K.55, A:T.56, A:T.56, A:T.56, A:A.57 Salt bridges: A:K.55, A:K.55, B:R.173, B:R.173, B:R.173, B:R.174 ATP.7: 21 residues within 4Å: Chain B: R.350, I.351, I.352, 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, R.545 Ligands: MG.6 20 PLIP interactions: 17 interactions with chain B, 3 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:T.393, B:E.394, B:N.500, B:R.607, C:E.476, C:E.476 Salt bridges: B:K.392, B:K.392, B:R.604, B:R.604, B:R.604, C:R.545 ATP.8: 22 residues within 4Å: Chain B: D.21, P.22, V.23, I.24, R.26, G.52, V.53, G.54, K.55, T.56, A.57, E.60, T.157, I.191, L.195, P.229, I.233 Chain C: K.42, A.170, R.173, R.174 Ligands: MG.5 17 PLIP interactions: 5 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:K.42, B:I.24, B:R.26, B:G.52, B:V.53, B:G.54, B:K.55, B:T.56, B:T.56, B:A.57, B:E.60 Salt bridges: C:R.173, C:R.173, C:R.173, C:R.174, B:K.55, B:K.55 ATP.9: 25 residues within 4Å: Chain C: D.21, P.22, V.23, I.24, G.25, R.26, 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 D: K.42, R.147, R.173, R.174 Ligands: MG.10 17 PLIP interactions: 5 interactions with chain D, 12 interactions with chain C Hydrogen bonds: D:R.147, C:I.24, C:G.25, C:G.52, C:G.54, C:K.55, C:T.56, C:A.57, C:T.157, C:Y.199, C:Y.199 Salt bridges: D:R.173, D:R.173, D:R.173, D:R.174, C:K.55, C:K.55 ATP.12: 21 residues within 4Å: Chain C: R.350, I.351, I.352, Q.354, 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 Chain D: R.377, E.476, R.545 Ligands: MG.11 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.352, C:G.389, C:V.390, C:G.391, C:K.392, C:T.393, C:T.393, C:E.394, C:E.394, C:N.500, D:R.377 Salt bridges: C:K.392, C:K.392, C:R.604, C:R.604, C:R.604, D:R.545 ATP.15: 23 residues within 4Å: Chain D: D.21, P.22, V.23, I.24, G.25, R.26, E.50, G.52, V.53, G.54, K.55, T.56, A.57, I.191, L.195, P.229, D.230, I.233 Chain E: K.42, R.147, R.173, R.174 Ligands: MG.14 19 PLIP interactions: 13 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:D.21, D:I.24, D:I.24, D:G.52, D:G.54, D:K.55, D:T.56, D:T.56, D:T.56, D:A.57, D:D.230, E:R.147 Salt bridges: D:K.55, D:K.55, E:R.147, E:R.173, E:R.173, E:R.173, E:R.174

3 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.13: 17 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, T.498, M.563, L.566, M.567, A.603, R.604, R.607 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:I.352, D:I.352, D:S.388, D:G.389, D:G.391, D:K.392, D:T.393, D:T.393, D:E.394, D:R.604, D:R.607, D:R.607 Salt bridges: D:K.392, D:K.392, D:R.604, D:R.604 ADP.16: 17 residues within 4Å: Chain E: D.21, P.22, V.23, I.24, R.26, P.51, G.52, V.53, G.54, K.55, T.56, A.57, I.191, L.195, I.233 Chain F: R.40, R.173 13 PLIP interactions: 3 interactions with chain F, 10 interactions with chain E Hydrogen bonds: F:R.40, E:D.21, E:I.24, E:G.52, E:V.53, E:G.54, E:G.54, E:K.55, E:T.56, E:A.57 Salt bridges: F:R.173, F:R.173, E:K.55 ADP.17: 20 residues within 4Å: Chain A: R.173 Chain F: D.21, P.22, V.23, I.24, G.25, R.26, E.50, G.52, V.53, G.54, K.55, T.56, A.57, E.60, I.191, L.195, P.229, D.230, I.233 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:I.24, F:R.26, F:E.50, F:G.52, F:G.54, F:K.55, F:T.56, F:A.57, F:E.60 Salt bridges: F:K.55, A:R.173

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

BO2.18: 14 residues within 4Å: Chain G: G.52, G.53, F.54, L.57, S.81, A.82, H.106, P.108, S.109, L.110, S.111, I.128, M.131, M.135 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:F.54, G:L.57, G:A.82, G:P.108, G:M.135 Hydrogen bonds: G:G.52, G:G.53, G:F.54, G:H.106, G:S.109, G:S.109 BO2.19: 14 residues within 4Å: Chain H: G.52, G.53, F.54, L.57, S.81, A.82, H.106, P.108, S.109, L.110, S.111, I.128, M.131, M.135 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:F.54, H:L.57, H:A.82, H:P.108, H:M.135 Hydrogen bonds: H:G.52, H:G.53, H:F.54, H:H.106, H:S.109, H:S.109 BO2.20: 14 residues within 4Å: Chain I: G.52, G.53, F.54, L.57, S.81, A.82, H.106, P.108, S.109, L.110, S.111, I.128, M.131, M.135 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:F.54, I:L.57, I:A.82, I:P.108, I:M.135 Hydrogen bonds: I:G.52, I:G.53, I:F.54, I:H.106, I:S.109, I:S.109 BO2.21: 14 residues within 4Å: Chain J: G.52, G.53, F.54, L.57, S.81, A.82, H.106, P.108, S.109, L.110, S.111, I.128, M.131, M.135 10 PLIP interactions: 10 interactions with chain J Hydrophobic interactions: J:F.54, J:L.57, J:P.108, J:M.135 Hydrogen bonds: J:G.52, J:G.53, J:F.54, J:H.106, J:S.109, J:S.109 BO2.22: 14 residues within 4Å: Chain K: G.52, G.53, F.54, L.57, S.81, A.82, H.106, P.108, S.109, L.110, S.111, I.128, M.131, M.135 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:F.54, K:L.57, K:A.82, K:P.108, K:M.135 Hydrogen bonds: K:G.52, K:G.53, K:F.54, K:S.109, K:S.109 BO2.23: 14 residues within 4Å: Chain L: G.52, G.53, F.54, L.57, S.81, A.82, H.106, P.108, S.109, L.110, S.111, I.128, M.131, M.135 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:F.54, L:L.57, L:A.82, L:P.108, L:M.135 Hydrogen bonds: L:G.52, L:G.53, L:F.54, L:H.106, L:S.109, L:S.109 BO2.24: 16 residues within 4Å: Chain M: G.51, G.52, G.53, F.54, L.57, S.81, A.82, H.106, Q.107, P.108, S.109, L.110, S.111, I.128, M.131, M.135 8 PLIP interactions: 8 interactions with chain M Hydrophobic interactions: M:F.54, M:L.57, M:L.110 Hydrogen bonds: M:G.52, M:F.54, M:A.82, M:S.109, M:S.109 BO2.25: 15 residues within 4Å: Chain G: F.118 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, N:P.111 Hydrogen bonds: N:G.55, N:G.55, N:I.57, N:L.112, N:L.112 BO2.26: 16 residues within 4Å: Chain H: F.118 Chain O: G.54, G.55, S.56, I.57, S.84, M.85, E.87, H.109, Q.110, P.111, L.112, G.113, F.129, I.132, M.136 10 PLIP interactions: 10 interactions with chain O Hydrophobic interactions: O:I.57, O:M.85, O:P.111, O:L.112 Hydrogen bonds: O:G.55, O:G.55, O:I.57, O:M.85, O:L.112, O:L.112 BO2.27: 15 residues within 4Å: Chain I: F.118 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 BO2.28: 16 residues within 4Å: Chain J: F.118 Chain Q: E.21, 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 Q Hydrophobic interactions: Q:I.57, Q:M.85, Q:P.111 Hydrogen bonds: Q:G.55, Q:G.55, Q:I.57, Q:M.85, Q:L.112 BO2.29: 16 residues within 4Å: Chain K: F.118 Chain R: E.21, 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 Hydrogen bonds: R:G.55, R:G.55, R:G.55, R:G.55, R:I.57, R:M.85, R:L.112 BO2.30: 16 residues within 4Å: Chain L: F.118 Chain S: E.21, 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: 5 interactions with chain S, 1 interactions with chain L Hydrophobic interactions: S:I.57, S:P.111 Hydrogen bonds: S:G.55, S:I.57, S:L.112 pi-Stacking: L:F.118 BO2.31: 17 residues within 4Å: Chain M: F.118 Chain T: E.21, G.54, G.55, S.56, I.57, S.84, M.85, E.87, 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
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
a

ATP-dependent Clp protease ATP-binding subunit ClpC1

ATP-dependent Clp protease proteolytic subunit 2

ATP-dependent Clp protease proteolytic subunit 1

Beta-casein

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