SMTL ID : 8ikt.1

Ternary trans-complex of phospho-parkin with cis ACT and pUb

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.178, H.182, C.214, A.216, C.218 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.178, A:H.182, A:C.214, A:C.218 ZN.2: 4 residues within 4Å: Chain A: C.290, C.293, H.298, C.302 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.290, A:C.293, A:H.298, A:C.302 ZN.3: 5 residues within 4Å: Chain A: C.91, T.93, C.94, C.121, C.126 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.91, A:C.94, A:C.121, A:C.126 ZN.4: 6 residues within 4Å: Chain A: C.163, T.165, C.166, R.170, C.185, C.188 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.163, A:C.166, A:C.185, A:C.188 ZN.5: 4 residues within 4Å: Chain A: C.257, C.262, C.277, C.285 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.257, A:C.262, A:C.277, A:C.285 ZN.6: 4 residues within 4Å: Chain A: C.75, C.79, C.137, H.140 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.75, A:C.79, A:C.137, A:H.140

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: S.143 Chain C: F.4, H.11, G.12, I.66 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.142, C:H.11, C:G.12 GOL.10: 2 residues within 4Å: Chain C: P.14, E.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.16

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 7 residues within 4Å: Chain A: K.224, E.225, L.226, H.227 Chain B: F.45, D.58, Y.59 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.45, B:Y.59, A:L.226 Hydrogen bonds: A:K.224, A:L.226

1 x 3CN: 3-AMINOPROPANE(Covalent)

3CN.9: 3 residues within 4Å: Chain A: C.272 Chain B: R.74, G.75 No protein-ligand interaction detected (PLIP)

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
E3 ubiquitin-protein ligase parkin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E3 ubiquitin-protein ligase parkin

Ubiquitin

E3 ubiquitin-protein ligase parkin

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