SMTL ID : 8ypa.1

Human mitochondrial ClpP in complex with TR89

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

homo-heptamer

Ligands

7 x 01: (6~{R})-2-[[3,5-bis(fluoranyl)phenyl]methyl]-6-(hydroxymethyl)-5-[[4-(trifluoromethyl)phenyl]methyl]-7,8-dihydro-6~{H}-pyrazolo[1,5-a][1,4]diazepin-4-one

01.1: 7 residues within 4Å: Chain A: I.46, L.50, F.51, Q.53, S.54, T.81, Y.84 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.50, A:L.50, A:T.81, A:Y.84 Hydrogen bonds: A:Q.53, A:Y.84 pi-Stacking: A:Y.84 01.2: 15 residues within 4Å: Chain B: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 Chain G: I.46, L.50, F.51, S.54, T.81, Y.84 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain G Hydrophobic interactions: B:L.25, B:E.28, B:I.30, B:Y.64, B:W.92, B:L.116, G:L.50, G:T.81, G:Y.84 Hydrogen bonds: B:Y.64, G:Q.53 Halogen bonds: B:R.24 pi-Stacking: G:Y.84 01.3: 15 residues within 4Å: Chain C: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 Chain F: I.46, L.50, F.51, S.54, T.81, Y.84 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: C:E.28, C:I.30, C:Y.64, C:W.92, C:L.116, F:L.50, F:Y.84 pi-Stacking: C:W.92, F:Y.84 Halogen bonds: C:R.24 01.4: 16 residues within 4Å: Chain C: I.46, L.50, F.51, Q.53, S.54, T.81, Y.84 Chain D: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:L.50, C:L.50, C:T.81, D:L.25, D:E.28, D:I.30, D:W.92, D:L.116 Hydrogen bonds: C:Q.53, D:E.28, D:E.28 pi-Stacking: C:Y.84, D:Y.64 Halogen bonds: D:R.24 01.5: 5 residues within 4Å: Chain D: I.46, F.51, S.54, T.81, Y.84 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.84 pi-Stacking: D:Y.84 01.6: 17 residues within 4Å: Chain B: I.46, L.50, F.51, Q.53, S.54, D.80, T.81, Y.84 Chain F: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 16 PLIP interactions: 10 interactions with chain F, 6 interactions with chain B Hydrophobic interactions: F:L.25, F:E.28, F:I.30, F:W.92, F:L.116, F:L.116, B:I.46, B:L.50, B:Y.84 Hydrogen bonds: F:E.28, F:E.28, B:Q.53 pi-Stacking: F:Y.64, B:Y.84 Halogen bonds: F:R.24, B:D.80 01.7: 16 residues within 4Å: Chain E: I.46, L.50, F.51, Q.53, S.54, T.81, Y.84 Chain G: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 14 PLIP interactions: 11 interactions with chain G, 3 interactions with chain E Hydrophobic interactions: G:L.25, G:E.28, G:I.30, G:Y.64, G:W.92, G:L.116, G:L.116, E:L.50 Hydrogen bonds: G:E.28, G:Y.64, E:Q.53 pi-Stacking: G:Y.64, E:Y.84 Halogen bonds: G:R.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Q.-N. et al., Human mitochondrial ClpP in complex with TR89. To Be Published

Release Date

2025-03-19

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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