SMTL ID : 8wzn.1

ParkinK211N in complex with phospho NEDD8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.225, A:C.228, A:H.233, A:C.237 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: 5 residues within 4Å: Chain A: C.26, C.29, C.56, S.58, 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: 5 residues within 4Å: Chain A: C.98, 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 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 PEG: DI(HYDROXYETHYL)ETHER

PEG.9: 3 residues within 4Å: Chain A: A.151, G.152, C.153 No protein-ligand interaction detected (PLIP) PEG.10: 3 residues within 4Å: Chain A: R.94, N.95, T.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.93, A:N.95 PEG.11: 5 residues within 4Å: Chain A: T.100, C.123, L.126, Y.127, V.150 No protein-ligand interaction detected (PLIP)

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

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