SMTL ID : 8w31.1

Crystal structure of parkin (R0RB):2pUb with activator compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-2-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.11, C.15, C.73, H.76 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.11, A:C.15, A:C.73, A:H.76 ZN.2: 4 residues within 4Å: Chain A: C.114, H.118, C.150, C.154 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.114, A:H.118, A:C.150, A:C.154 ZN.3: 5 residues within 4Å: Chain A: R.209, C.226, C.229, H.234, C.238 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.226, A:C.229, A:H.234, A:C.238 ZN.4: 4 residues within 4Å: Chain A: C.27, C.30, C.57, C.62 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.27, A:C.30, A:C.57, A:C.62 ZN.5: 4 residues within 4Å: Chain A: C.99, C.102, C.121, C.124 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.99, A:C.102, A:C.121, A:C.124 ZN.6: 4 residues within 4Å: Chain A: C.193, C.198, C.213, C.221 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.193, A:C.198, A:C.213, A:C.221

1 x 01: (S)-1-(6-benzyl-3-(4-(1,2,3,4-tetrahydroquinoline-1-carbonyl)phenyl)-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl)ethan-1-one

01.7: 15 residues within 4Å: Chain A: S.5, F.7, L.23, V.25, L.37, G.40, P.41, S.42, C.43, W.44, F.69 Chain C: A.46, G.47, K.48 Ligands: GOL.8 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.7, A:F.7, A:L.23, A:V.25, A:L.37, A:P.41, A:P.41, A:F.69, C:K.48 pi-Stacking: A:W.44

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: G.21, K.22, L.23, R.24 Chain C: N.60 Ligands: 01.7 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:N.60, A:G.21, A:L.23, A:R.24, A:R.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauve, V. et al., Activation of parkin by a molecular glue. Nat Commun (2024)

Release Date

2024-08-21

Peptides

E3 ubiquitin-protein ligase parkin: A
Ubiquitin: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E3 ubiquitin-protein ligase parkin

Ubiquitin

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