SMTL ID : 6hwm.1

Structure of Thermus thermophilus ClpP in complex with bortezomib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-14-mer

Ligands

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

BO2.1: 14 residues within 4Å: Chain A: P.66, G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, G.126, I.142, L.149 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.69, A:V.70, A:P.124, A:W.125, A:L.149 Hydrogen bonds: A:G.68, A:G.68, A:G.68, A:G.68, A:V.70, A:M.98, A:W.125, A:W.125 BO2.2: 13 residues within 4Å: Chain B: P.66, G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, I.142, L.149 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:E.69, B:V.70, B:W.125, B:L.149 Hydrogen bonds: B:G.68, B:G.68, B:G.68, B:V.70, B:M.98, B:W.125, B:W.125, B:W.125 pi-Stacking: B:W.125 BO2.3: 13 residues within 4Å: Chain C: P.66, G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, I.142, L.149 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:E.69, C:M.98, C:P.124, C:W.125 Hydrogen bonds: C:G.68, C:G.68, C:G.68, C:V.70, C:M.98, C:W.125, C:W.125, C:W.125 pi-Stacking: C:W.125 BO2.5: 13 residues within 4Å: Chain D: G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, G.126, I.142, L.149 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:E.69, D:V.70, D:P.124, D:W.125 Hydrogen bonds: D:G.68, D:G.68, D:G.68, D:V.70, D:M.98, D:W.125, D:W.125, D:W.125 pi-Stacking: D:W.125 BO2.6: 12 residues within 4Å: Chain E: G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, I.142, L.149 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:V.70, E:P.124, E:W.125, E:L.149 Hydrogen bonds: E:G.68, E:G.68, E:G.68, E:V.70, E:M.98, E:W.125, E:W.125, E:W.125 BO2.8: 13 residues within 4Å: Chain F: P.66, G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, I.142, L.149 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:E.69, F:V.70, F:W.125, F:L.149 Hydrogen bonds: F:G.68, F:G.68, F:G.68, F:V.70, F:M.98, F:W.125, F:W.125, F:W.125 pi-Stacking: F:W.125 BO2.9: 12 residues within 4Å: Chain G: G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, I.142, L.149 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:E.69, G:P.124, G:W.125, G:L.149 Hydrogen bonds: G:G.68, G:G.68, G:G.68, G:V.70, G:M.98, G:W.125, G:W.125, G:W.125 pi-Stacking: G:W.125 BO2.11: 14 residues within 4Å: Chain H: P.66, G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, G.126, I.142, L.149 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:E.69, H:V.70, H:P.124, H:W.125, H:L.149 Hydrogen bonds: H:G.68, H:G.68, H:G.68, H:G.68, H:V.70, H:M.98, H:W.125, H:W.125 BO2.12: 13 residues within 4Å: Chain I: P.66, G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, I.142, L.149 13 PLIP interactions: 13 interactions with chain I Hydrophobic interactions: I:E.69, I:V.70, I:W.125, I:L.149 Hydrogen bonds: I:G.68, I:G.68, I:G.68, I:V.70, I:M.98, I:W.125, I:W.125, I:W.125 pi-Stacking: I:W.125 BO2.13: 13 residues within 4Å: Chain J: P.66, G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, I.142, L.149 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:E.69, J:M.98, J:P.124, J:W.125 Hydrogen bonds: J:G.68, J:G.68, J:G.68, J:V.70, J:M.98, J:W.125, J:W.125, J:W.125 pi-Stacking: J:W.125 BO2.15: 13 residues within 4Å: Chain K: G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, G.126, I.142, L.149 13 PLIP interactions: 13 interactions with chain K Hydrophobic interactions: K:E.69, K:V.70, K:P.124, K:W.125 Hydrogen bonds: K:G.68, K:G.68, K:G.68, K:V.70, K:M.98, K:W.125, K:W.125, K:W.125 pi-Stacking: K:W.125 BO2.16: 12 residues within 4Å: Chain L: G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, I.142, L.149 12 PLIP interactions: 12 interactions with chain L Hydrophobic interactions: L:V.70, L:P.124, L:W.125, L:L.149 Hydrogen bonds: L:G.68, L:G.68, L:G.68, L:V.70, L:M.98, L:W.125, L:W.125, L:W.125 BO2.18: 13 residues within 4Å: Chain M: P.66, G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, I.142, L.149 13 PLIP interactions: 13 interactions with chain M Hydrophobic interactions: M:E.69, M:V.70, M:W.125, M:L.149 Hydrogen bonds: M:G.68, M:G.68, M:G.68, M:V.70, M:M.98, M:W.125, M:W.125, M:W.125 pi-Stacking: M:W.125 BO2.19: 12 residues within 4Å: Chain N: G.67, G.68, E.69, V.70, S.97, M.98, H.122, Q.123, P.124, W.125, I.142, L.149 13 PLIP interactions: 13 interactions with chain N Hydrophobic interactions: N:E.69, N:P.124, N:W.125, N:L.149 Hydrogen bonds: N:G.68, N:G.68, N:G.68, N:V.70, N:M.98, N:W.125, N:W.125, N:W.125 pi-Stacking: N:W.125

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain C: T.157, G.158, E.181, G.183 No protein-ligand interaction detected (PLIP) PEG.7: 3 residues within 4Å: Chain E: T.157, E.181, Y.182 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.158 PEG.10: 4 residues within 4Å: Chain G: T.157, G.158, L.180, E.181 No protein-ligand interaction detected (PLIP) PEG.14: 4 residues within 4Å: Chain J: T.157, G.158, E.181, G.183 No protein-ligand interaction detected (PLIP) PEG.17: 3 residues within 4Å: Chain L: T.157, E.181, Y.182 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:G.158 PEG.20: 4 residues within 4Å: Chain N: T.157, G.158, L.180, E.181 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Felix, J. et al., Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Sci Adv (2019)

Release Date

2019-09-18

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
A

I
B

J
C

K
D

L
E

M
F

N
G

ATP-dependent Clp protease proteolytic subunit

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