SMTL ID : 7uvr.1

Crystal structure of human ClpP protease in complex with TR-65

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

homo-14-mer

Ligands

14 x PJF: 3-{[(10R)-4-[(4-chlorophenyl)methyl]-5-oxo-1,2,4,5,8,9-hexahydroimidazo[1,2-a]pyrido[3,4-e]pyrimidin-7(6H)-yl]methyl}benzonitrile(Non-covalent)

PJF.1: 15 residues within 4Å: Chain A: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 Chain G: I.44, L.48, F.49, S.52, T.79, Y.82 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain G Hydrophobic interactions: A:L.23, A:E.26, A:I.28, A:Y.62, A:V.92, A:L.114, G:I.44, G:L.48 Hydrogen bonds: A:E.26, A:E.26 pi-Stacking: G:Y.82 PJF.2: 15 residues within 4Å: Chain A: I.44, L.48, F.49, S.52, T.79, Y.82 Chain B: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.23, B:E.26, B:I.28, B:Y.62, B:L.114, A:L.48, A:L.48 Hydrogen bonds: B:E.26, A:Q.51 pi-Stacking: A:Y.82 PJF.3: 15 residues within 4Å: Chain B: I.44, L.48, F.49, S.52, T.79, Y.82 Chain C: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:L.48, B:L.48, C:L.23, C:E.26, C:I.28, C:Y.62, C:W.90, C:L.114 pi-Stacking: B:Y.82 Hydrogen bonds: C:E.26, C:E.26 PJF.4: 15 residues within 4Å: Chain C: I.44, L.48, F.49, S.52, T.79, Y.82 Chain D: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:I.44, C:L.48, D:L.23, D:E.26, D:I.28, D:L.114 Water bridges: C:Q.51 pi-Stacking: C:Y.82, D:H.60 Hydrogen bonds: D:E.26 PJF.5: 13 residues within 4Å: Chain D: I.44, L.48, F.49, S.52, T.79, Y.82 Chain E: R.22, L.23, E.26, H.60, Y.62, W.90, V.92 13 PLIP interactions: 6 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:L.23, E:E.26, E:Y.62, E:Y.62, D:I.44, D:L.48, D:L.48, D:L.48, D:T.79 Hydrogen bonds: E:Y.62 pi-Stacking: E:H.60, D:Y.82 Water bridges: D:Q.51 PJF.6: 15 residues within 4Å: Chain E: I.44, L.48, F.49, S.52, T.79, Y.82 Chain F: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:L.23, F:E.26, F:Y.62, F:L.114, E:L.48 Hydrogen bonds: F:Y.62 pi-Stacking: F:H.60, E:Y.82 PJF.7: 16 residues within 4Å: Chain F: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain G: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 13 PLIP interactions: 7 interactions with chain G, 6 interactions with chain F Hydrophobic interactions: G:L.23, G:E.26, G:I.28, G:Y.62, G:L.114, F:I.44, F:L.48, F:L.48, F:T.79 Hydrogen bonds: G:Y.62, F:Q.51 pi-Stacking: G:H.60, F:Y.82 PJF.8: 15 residues within 4Å: Chain H: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 Chain N: I.44, L.48, F.49, S.52, T.79, Y.82 11 PLIP interactions: 3 interactions with chain N, 8 interactions with chain H Hydrophobic interactions: N:I.44, N:L.48, H:L.23, H:E.26, H:I.28, H:Y.62, H:V.92, H:L.114 pi-Stacking: N:Y.82 Hydrogen bonds: H:E.26, H:Y.62 PJF.9: 15 residues within 4Å: Chain H: I.44, L.48, F.49, S.52, T.79, Y.82 Chain I: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 10 PLIP interactions: 4 interactions with chain H, 6 interactions with chain I Hydrophobic interactions: H:L.48, H:L.48, I:L.23, I:E.26, I:I.28, I:Y.62, I:L.114 Hydrogen bonds: H:Q.51, I:Y.62 pi-Stacking: H:Y.82 PJF.10: 15 residues within 4Å: Chain I: I.44, L.48, F.49, S.52, T.79, Y.82 Chain J: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 11 PLIP interactions: 3 interactions with chain I, 8 interactions with chain J Hydrophobic interactions: I:L.48, I:L.48, J:L.23, J:E.26, J:I.28, J:Y.62, J:W.90, J:L.114 pi-Stacking: I:Y.82 Hydrogen bonds: J:E.26, J:Y.62 PJF.11: 15 residues within 4Å: Chain J: I.44, L.48, F.49, S.52, T.79, Y.82 Chain K: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 10 PLIP interactions: 6 interactions with chain K, 4 interactions with chain J Hydrophobic interactions: K:L.23, K:E.26, K:I.28, K:L.114, J:I.44, J:L.48 Hydrogen bonds: K:Y.62 pi-Stacking: K:H.60, J:Y.82 Water bridges: J:Q.51 PJF.12: 13 residues within 4Å: Chain K: I.44, L.48, F.49, S.52, T.79, Y.82 Chain L: R.22, L.23, E.26, H.60, Y.62, W.90, V.92 13 PLIP interactions: 7 interactions with chain K, 6 interactions with chain L Hydrophobic interactions: K:I.44, K:L.48, K:L.48, K:L.48, K:T.79, L:L.23, L:E.26, L:Y.62, L:Y.62 Water bridges: K:Q.51 pi-Stacking: K:Y.82, L:H.60 Hydrogen bonds: L:E.26 PJF.13: 15 residues within 4Å: Chain L: I.44, L.48, F.49, S.52, T.79, Y.82 Chain M: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 8 PLIP interactions: 6 interactions with chain M, 2 interactions with chain L Hydrophobic interactions: M:L.23, M:E.26, M:Y.62, M:L.114, L:L.48 Hydrogen bonds: M:E.26 pi-Stacking: M:H.60, L:Y.82 PJF.14: 16 residues within 4Å: Chain M: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain N: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 13 PLIP interactions: 7 interactions with chain N, 6 interactions with chain M Hydrophobic interactions: N:L.23, N:E.26, N:I.28, N:Y.62, N:L.114, M:I.44, M:L.48, M:L.48, M:T.79 Hydrogen bonds: N:E.26, M:Q.51 pi-Stacking: N:H.60, M:Y.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mabanglo, M.F. et al., Potent ClpP agonists with anticancer properties bind with improved structural complementarity and alter the mitochondrial N-terminome. Structure (2023)

Release Date

2023-01-11

Peptides

ATP-dependent Clp protease proteolytic subunit, mitochondrial: 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, mitochondrial

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