SMTL ID : 8ikv.1 (1 other biounit)

pUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-mer

Ligands

8 x ZN: ZINC ION

ZN.1: 5 residues within 4Å: Chain A: C.28, T.30, C.31, C.58, C.63 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.28, A:C.31, A:C.58, A:C.63 ZN.2: 4 residues within 4Å: Chain A: C.227, C.230, H.235, C.239 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.227, A:C.230, A:H.235, A:C.239 ZN.3: 4 residues within 4Å: Chain A: C.115, H.119, C.151, C.155 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.115, A:H.119, A:C.151, A:C.155 ZN.4: 4 residues within 4Å: Chain A: C.308, C.311, C.319, H.323 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.308, A:C.311, A:C.319, A:H.323 ZN.5: 5 residues within 4Å: Chain A: C.100, T.102, C.103, C.122, C.125 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.100, A:C.103, A:C.122, A:C.125 ZN.6: 4 residues within 4Å: Chain A: C.194, C.199, C.214, C.222 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.194, A:C.199, A:C.214, A:C.222 ZN.7: 4 residues within 4Å: Chain A: C.280, C.283, C.298, C.303 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.280, A:C.283, A:C.298, A:C.303 ZN.8: 4 residues within 4Å: Chain A: C.12, C.16, C.74, H.77 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.12, A:C.16, A:C.74, A:H.77

2 x PEG: DI(HYDROXYETHYL)ETHER

PEG.9: 2 residues within 4Å: Chain A: R.196, F.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.196, A:R.196 PEG.10: 4 residues within 4Å: Chain A: W.45, H.89, V.112, Q.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lenka, D.R. et al., Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans. Elife (2024)

Release Date

2024-09-11

Peptides

E3 ubiquitin-protein ligase parkin: A
Ubiquitin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

E3 ubiquitin-protein ligase parkin

Ubiquitin

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