SMTL ID : 6bba.1

Crystal structure of human mitochondrial ClpP complex with acyldepsipeptide ADEP-28

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-heptamer

Ligands

7 x SHV- WFP- ALO- PRO- 3A0- ALA- PRO: Acyldepsipeptide ADEP-28(Non-covalent)

SHV-WFP-ALO-PRO-3A0-ALA-PRO.1: 17 residues within 4Å: Chain A: R.22, L.23, I.28, H.60, Y.62, C.88, W.90, L.114, K.187, L.189, P.192 Chain G: I.44, L.48, F.49, S.52, T.79, Y.82 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain G Hydrophobic interactions: A:L.189, A:R.22, A:L.23, G:F.49, A:Y.62, A:W.90, A:L.114, G:L.48, G:T.79, G:Y.82 Hydrogen bonds: A:Y.62, A:Y.62 pi-Stacking: A:W.90 SHV-WFP-ALO-PRO-3A0-ALA-PRO.2: 20 residues within 4Å: Chain A: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain B: R.22, L.23, E.26, I.28, H.60, Y.62, C.88, W.90, V.92, L.114, K.187, L.189, P.192 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.189, A:L.48, A:F.49, B:L.23, B:E.26, A:L.48, B:Y.62, B:W.90, B:V.92, B:L.114 Hydrogen bonds: A:Q.51, A:Q.51, B:Y.62 pi-Stacking: A:Y.82, B:W.90 SHV-WFP-ALO-PRO-3A0-ALA-PRO.3: 20 residues within 4Å: Chain B: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain C: R.22, E.26, I.28, H.60, Y.62, C.88, W.90, V.92, H.112, L.114, K.187, L.189, P.192 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.189, C:R.22, C:E.26, C:I.28, B:L.48, B:L.48, B:F.49, B:L.48, B:Y.82, C:Y.62, C:W.90, C:L.114 Hydrogen bonds: B:Q.51, C:Y.62 pi-Stacking: C:W.90 SHV-WFP-ALO-PRO-3A0-ALA-PRO.4: 19 residues within 4Å: Chain C: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain D: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, H.112, L.114, K.187, L.189, P.192 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.189, C:F.49, D:R.22, D:L.23, D:Y.62, D:W.90, D:L.114, C:L.48, C:L.48, C:Y.82 Hydrogen bonds: C:Q.51, D:Y.62 pi-Stacking: D:W.90 SHV-WFP-ALO-PRO-3A0-ALA-PRO.5: 20 residues within 4Å: Chain D: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain E: R.22, E.26, I.28, H.60, Y.62, C.88, W.90, V.92, H.112, L.114, K.187, L.189, P.192 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:L.189, D:L.48, D:F.49, E:R.22, E:E.26, E:Y.62, E:W.90, D:L.48, D:Y.82 Hydrogen bonds: D:Q.51, D:Q.51, E:Y.62 pi-Stacking: E:W.90 SHV-WFP-ALO-PRO-3A0-ALA-PRO.6: 17 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, H.112, L.114, L.189, P.192 11 PLIP interactions: 6 interactions with chain F, 5 interactions with chain E Hydrophobic interactions: F:L.189, F:R.22, F:L.23, F:E.26, E:F.49, F:Y.62, F:W.90, F:L.114, E:I.44, E:L.48, E:L.48, E:T.79, E:Y.82 Hydrogen bonds: E:Q.51, F:Y.62, F:Y.62 pi-Stacking: F:W.90 SHV-WFP-ALO-PRO-3A0-ALA-PRO.7: 19 residues within 4Å: Chain F: I.44, L.48, F.49, S.52, T.79, Y.82 Chain G: R.22, L.23, E.26, I.28, H.60, Y.62, C.88, W.90, V.92, L.114, K.187, L.189, P.192 11 PLIP interactions: 7 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:L.189, G:R.22, G:L.23, G:E.26, F:L.48, F:F.49, G:W.90, G:V.92, G:L.114, F:L.48, F:L.48, F:T.79, F:Y.82 Hydrogen bonds: F:Q.51, F:Q.51, G:Y.62, G:Y.62 pi-Stacking: G:Y.62, G:W.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wong, K.S. et al., Acyldepsipeptide Analogs Dysregulate Human Mitochondrial ClpP Protease Activity and Cause Apoptotic Cell Death. Cell Chem Biol (2018)

Release Date

2018-07-11

Peptides

ATP-dependent Clp protease proteolytic subunit, mitochondrial: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ATP-dependent Clp protease proteolytic subunit, mitochondrial

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