SMTL ID : 8hgk.1

Crystal structure of human ClpP in complex with ZK53

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-14-mer

Ligands

14 x ZLL: 4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide(Non-covalent)

ZLL.1: 14 residues within 4Å: Chain A: L.24, E.27, I.29, H.61, Y.63, W.91, V.93, L.115 Chain G: I.45, L.49, F.50, S.53, T.80, Y.83 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:L.24, A:E.27, A:I.29, A:Y.63, A:L.115 Water bridges: G:Q.52 pi-Stacking: G:Y.83 ZLL.2: 14 residues within 4Å: Chain A: I.45, L.49, F.50, S.53, T.80, Y.83 Chain B: L.24, E.27, I.29, H.61, Y.63, W.91, V.93, L.115 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.24, B:E.27, B:I.29, B:Y.63, B:L.115 pi-Stacking: A:Y.83 ZLL.4: 13 residues within 4Å: Chain B: I.45, L.49, F.50, S.53, T.80, Y.83 Chain C: L.24, E.27, I.29, H.61, Y.63, W.91, V.93 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.24, C:E.27, C:I.29, C:Y.63, C:V.93 pi-Stacking: B:Y.83 ZLL.5: 14 residues within 4Å: Chain C: I.45, L.49, F.50, S.53, T.80, Y.83 Chain D: L.24, E.27, I.29, H.61, Y.63, W.91, V.93, L.115 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:E.27, D:I.29, D:Y.63, D:V.93, D:L.115 Hydrogen bonds: D:Y.63 pi-Stacking: C:Y.83 ZLL.6: 13 residues within 4Å: Chain D: I.45, L.49, F.50, S.53, T.80, Y.83 Chain E: L.24, E.27, H.61, Y.63, W.91, V.93, L.115 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E Water bridges: D:Q.52 pi-Stacking: D:Y.83 Hydrophobic interactions: E:E.27, E:Y.63, E:L.115 Hydrogen bonds: E:Y.63 ZLL.8: 13 residues within 4Å: Chain E: I.45, L.49, F.50, S.53, T.80, Y.83 Chain F: L.24, E.27, H.61, Y.63, W.91, V.93, L.115 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:L.24, F:E.27, F:Y.63, F:V.93, F:L.115 Hydrogen bonds: F:Y.63 pi-Stacking: E:Y.83 ZLL.10: 15 residues within 4Å: Chain F: I.45, L.49, F.50, S.53, T.80, Y.83 Chain G: R.23, L.24, E.27, I.29, H.61, Y.63, W.91, V.93, L.115 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:E.27, G:I.29, G:Y.63, G:V.93, G:L.115 pi-Stacking: F:Y.83 ZLL.12: 13 residues within 4Å: Chain H: L.24, E.27, H.61, Y.63, W.91, V.93, L.115 Chain N: I.45, L.49, F.50, S.53, T.80, Y.83 6 PLIP interactions: 2 interactions with chain N, 4 interactions with chain H Water bridges: N:Q.52 pi-Stacking: N:Y.83 Hydrophobic interactions: H:E.27, H:Y.63, H:V.93, H:L.115 ZLL.13: 14 residues within 4Å: Chain H: I.45, L.49, F.50, S.53, T.80, Y.83 Chain I: L.24, E.27, I.29, H.61, Y.63, W.91, V.93, L.115 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:E.27, I:Y.63 pi-Stacking: H:Y.83 ZLL.14: 13 residues within 4Å: Chain I: I.45, F.50, S.53, T.80, Y.83 Chain J: R.23, L.24, E.27, H.61, Y.63, W.91, V.93, L.115 8 PLIP interactions: 6 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:L.24, J:E.27, J:Y.63, J:V.93, J:L.115 Hydrogen bonds: J:Y.63 Water bridges: I:Q.52 pi-Stacking: I:Y.83 ZLL.15: 14 residues within 4Å: Chain J: I.45, F.50, S.53, T.80, Y.83 Chain K: R.23, L.24, E.27, I.29, H.61, Y.63, W.91, V.93, L.115 7 PLIP interactions: 5 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: K:E.27, K:I.29, K:Y.63, K:V.93 Hydrogen bonds: K:Y.63 Water bridges: J:Q.52 pi-Stacking: J:Y.83 ZLL.16: 13 residues within 4Å: Chain L: I.45, L.49, S.53, T.80, Y.83 Chain M: L.24, E.27, I.29, H.61, Y.63, W.91, V.93, L.115 7 PLIP interactions: 1 interactions with chain L, 6 interactions with chain M pi-Stacking: L:Y.83 Hydrophobic interactions: M:L.24, M:E.27, M:I.29, M:Y.63, M:V.93, M:L.115 ZLL.17: 12 residues within 4Å: Chain K: I.45, L.49, F.50, S.53, T.80, Y.83 Chain L: E.27, H.61, Y.63, W.91, V.93, L.115 6 PLIP interactions: 4 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:E.27, L:Y.63, L:L.115 Hydrogen bonds: L:Y.63 Water bridges: K:Q.52 pi-Stacking: K:Y.83 ZLL.19: 13 residues within 4Å: Chain M: I.45, L.49, S.53, T.80, Y.83 Chain N: L.24, E.27, I.29, H.61, Y.63, W.91, V.93, L.115 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: N:E.27, N:I.29, N:Y.63 pi-Stacking: M:Y.83

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: H.123, P.125, D.172 Chain H: Q.139 Chain I: S.126, D.172 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: I:D.172, A:H.123, H2O.1, H2O.11 MG.7: 1 residues within 4Å: Chain E: D.172 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:D.172, H2O.5, H2O.6, H2O.6, H2O.15, H2O.15 MG.9: 1 residues within 4Å: Chain F: D.172 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:D.172, H2O.7, H2O.8, H2O.8, H2O.13, H2O.15 MG.11: 2 residues within 4Å: Chain G: H.123, D.172 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.172, H2O.9, H2O.11, H2O.12 MG.18: 3 residues within 4Å: Chain D: D.172 Chain M: H.123, D.172 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.172, H2O.4, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, L.L. et al., Selective activator of human ClpP triggers cell cycle arrest to inhibit lung squamous cell carcinoma. Nat Commun (2023)

Release Date

2023-09-27

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
H

I
I

J
J

K
K

L
L

M
M

N
N

ATP-dependent Clp protease proteolytic subunit, mitochondrial