SMTL ID : 7uvn.1

Crystal structure of human ClpP protease in complex with TR-57

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

homo-14-mer

Ligands

14 x P3O: 3-({3-[(4-chlorophenyl)methyl]-1-methyl-2,4-dioxo-1,3,4,5,7,8-hexahydropyrido[4,3-d]pyrimidin-6(2H)-yl}methyl)benzonitrile(Non-covalent)

P3O.1: 15 residues within 4Å: Chain A: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92 Chain G: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain G Hydrophobic interactions: A:L.23, A:E.26, A:Y.62, G:L.48, G:L.48, G:L.48 pi-Stacking: G:Y.82 P3O.2: 13 residues within 4Å: Chain A: 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 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.23, B:E.26, B:Y.62, A:L.48, A:L.48, A:L.48 Hydrogen bonds: B:E.26 Water bridges: A:Q.51 pi-Stacking: A:Y.82 P3O.3: 16 residues within 4Å: Chain B: I.44, L.48, F.49, Q.51, 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 9 PLIP interactions: 4 interactions with chain B, 5 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:L.114 Hydrogen bonds: B:Q.51 pi-Stacking: B:Y.82 P3O.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 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.23, D:E.26, D:Y.62, D:V.92, D:L.114, C:L.48 Hydrogen bonds: D:Y.62 pi-Stacking: C:Y.82 P3O.5: 14 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, I.28, H.60, Y.62, W.90, V.92 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:L.48, D:L.48, D:L.48, E:L.23, E:E.26, E:Y.62 pi-Stacking: D:Y.82 Hydrogen bonds: E:Y.62 P3O.6: 14 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 9 PLIP interactions: 5 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:L.23, F:E.26, F:Y.62, F:V.92, E:L.48, E:L.48, E:L.48 Hydrogen bonds: F:Y.62 pi-Stacking: E:Y.82 P3O.7: 15 residues within 4Å: Chain F: 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 9 PLIP interactions: 4 interactions with chain G, 5 interactions with chain F Hydrophobic interactions: G:L.23, G:E.26, G:Y.62, G:L.114, F:L.48, F:L.48, F:L.48 Hydrogen bonds: F:Q.51 pi-Stacking: F:Y.82 P3O.8: 15 residues within 4Å: Chain H: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92 Chain N: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 9 PLIP interactions: 5 interactions with chain H, 4 interactions with chain N Hydrophobic interactions: H:L.23, H:E.26, H:Y.62, N:L.48, N:L.48, N:L.48 Hydrogen bonds: H:E.26, H:Y.62 pi-Stacking: N:Y.82 P3O.9: 13 residues within 4Å: Chain H: 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 9 PLIP interactions: 4 interactions with chain I, 5 interactions with chain H Hydrophobic interactions: I:L.23, I:E.26, I:Y.62, H:L.48, H:L.48, H:L.48 Hydrogen bonds: I:Y.62 Water bridges: H:Q.51 pi-Stacking: H:Y.82 P3O.10: 16 residues within 4Å: Chain I: I.44, L.48, F.49, Q.51, 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 10 PLIP interactions: 6 interactions with chain J, 4 interactions with chain I Hydrophobic interactions: J:L.23, J:E.26, J:I.28, J:Y.62, J:L.114, I:L.48, I:L.48 Hydrogen bonds: J:Y.62, I:Q.51 pi-Stacking: I:Y.82 P3O.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 8 PLIP interactions: 6 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: K:L.23, K:E.26, K:Y.62, K:V.92, K:L.114, J:L.48 Hydrogen bonds: K:E.26 pi-Stacking: J:Y.82 P3O.12: 14 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, I.28, H.60, Y.62, W.90, V.92 8 PLIP interactions: 4 interactions with chain L, 4 interactions with chain K Hydrophobic interactions: L:L.23, L:E.26, L:Y.62, K:L.48, K:L.48, K:L.48 Hydrogen bonds: L:E.26 pi-Stacking: K:Y.82 P3O.13: 14 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 9 PLIP interactions: 5 interactions with chain M, 4 interactions with chain L Hydrophobic interactions: M:L.23, M:E.26, M:Y.62, M:V.92, L:L.48, L:L.48, L:L.48 Hydrogen bonds: M:E.26 pi-Stacking: L:Y.82 P3O.14: 15 residues within 4Å: Chain M: 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 11 PLIP interactions: 6 interactions with chain N, 5 interactions with chain M Hydrophobic interactions: N:L.23, N:E.26, N:Y.62, N:L.114, M:L.48, M:L.48, M:L.48 Hydrogen bonds: N:E.26, N:Y.62, M:Q.51 pi-Stacking: 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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