SMTL ID : 8wzo.1

Parkin in complex with phospho NEDD8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-mer

Ligands

8 x ZN: ZINC ION

ZN.1: 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.2: 4 residues within 4Å: Chain A: C.225, C.228, H.233, C.237 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.225, A:C.228, A:H.233 ZN.3: 4 residues within 4Å: Chain A: C.306, C.309, C.317, H.321 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.306, A:C.309, A:C.317, A:H.321 ZN.4: 4 residues within 4Å: Chain A: C.26, 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.5: 4 residues within 4Å: Chain A: C.98, C.101, 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 ZN.7: 4 residues within 4Å: Chain A: C.278, C.281, C.296, C.301 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.278, A:C.281, A:C.296, A:C.301 ZN.8: 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

3 x EDO: 1,2-ETHANEDIOL

EDO.9: 5 residues within 4Å: Chain A: R.135, Y.145, Y.178, E.181, E.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.135 EDO.10: 5 residues within 4Å: Chain A: V.46, P.49, A.66, E.67, F.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.46, A:F.68 Water bridges: A:N.50 EDO.11: 5 residues within 4Å: Chain A: V.24, L.34, T.35, L.36, W.322 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.36 Water bridges: A:L.34, A:L.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lenka, D.R. et al., Parkin in complex with phospho NEDD8. Structure

Release Date

2024-09-18

Peptides

E3 ubiquitin-protein ligase parkin: A
NEDD8: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E3 ubiquitin-protein ligase parkin

NEDD8

Related Entries With Identical Sequence