SMTL ID : 8ikm.1

Trans complex of phospho parkin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.10, C.14, C.72, H.75 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.10, A:C.14, A:C.72, A:H.75 ZN.2: 5 residues within 4Å: Chain A: C.26, T.28, C.29, C.56, C.61 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.26, A:C.29, A:C.56, A:C.61 ZN.3: 4 residues within 4Å: Chain A: C.113, H.117, C.149, C.153 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.113, A:H.117, A:C.149, A:C.153 ZN.4: 4 residues within 4Å: Chain A: C.225, C.228, H.233, C.237 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.225, A:C.228, A:H.233, A:C.237, H2O.1 ZN.5: 6 residues within 4Å: Chain A: C.98, T.100, C.101, R.105, C.120, C.123 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.98, A:C.101, A:C.120, A:C.123 ZN.6: 4 residues within 4Å: Chain A: C.192, C.197, C.212, C.220 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.192, A:C.197, A:C.212, A:C.220

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: K.159, E.160, L.161, H.162 Chain B: F.45, Y.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.162

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 7 residues within 4Å: Chain A: T.91, N.92, S.93, R.94, N.95, I.96, V.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.92, A:R.94, A:N.95

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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