SMTL ID : 8ik6.2 (1 other biounit)

pUbl depleted Parkin complex with pUbiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-mer

Ligands

6 x ZN: ZINC ION

ZN.1: 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 ZN.2: 6 residues within 4Å: Chain A: C.28, T.30, C.31, C.58, C.63, G.65 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.28, A:C.31, A:C.58, A:C.63 ZN.3: 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.4: 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.5: 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.6: 4 residues within 4Å: Chain A: C.100, 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

2 x SO4: SULFATE ION

SO4.7: 4 residues within 4Å: Chain A: S.3, I.4, Y.5, N.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.3, A:S.3, A:N.310 SO4.8: 4 residues within 4Å: Chain A: Q.40, G.41, C.293, H.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.41, A:H.295 Salt bridges: A:H.295

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
A

B
B

E3 ubiquitin-protein ligase parkin

Ubiquitin

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