SMTL ID : 8ik6.1 (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

8 x ZN: ZINC ION

ZN.1: 5 residues within 4Å: Chain A: C.115, H.119, C.151, A.153, 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.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.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.4: 4 residues within 4Å: Chain A: C.28, 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.5: 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 ZN.6: 5 residues within 4Å: Chain A: C.194, C.199, A.201, 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: 5 residues within 4Å: Chain A: C.280, R.282, 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: 5 residues within 4Å: Chain A: C.12, C.16, Q.20, 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

7 x SO4: SULFATE ION

SO4.9: 5 residues within 4Å: Chain A: K.13, R.167, E.171, N.175 Chain B: E.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.175 Salt bridges: A:K.13, A:R.167 SO4.10: 3 residues within 4Å: Chain A: R.25, K.73, T.79 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.79, A:T.79 Salt bridges: A:R.25, A:K.73 SO4.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.12: 4 residues within 4Å: Chain A: R.32 Chain B: E.18, P.19, S.20 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.32 Hydrogen bonds: B:E.18, B:S.20 SO4.13: 3 residues within 4Å: Chain A: S.43, G.291, G.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.43, A:S.43, A:G.292 SO4.14: 2 residues within 4Å: Chain A: N.116, P.156 No protein-ligand interaction detected (PLIP) SO4.15: 6 residues within 4Å: Chain A: T.39, Q.40, G.41, N.290, C.293, H.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.41, A:N.290 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
C

B
D

E3 ubiquitin-protein ligase parkin

Ubiquitin

Related Entries With Identical Sequence