SMTL ID : 4zyn.2 (1 other biounit)

Crystal Structure of Parkin E3 ubiquitin ligase (linker deletion; delta 86-130)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

monomer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.110, C.114, C.172, H.175 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.110, A:C.114, A:C.172, A:H.175 ZN.2: 5 residues within 4Å: Chain A: C.126, C.129, C.156, S.158, C.161 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.126, A:C.129, A:C.156, A:C.161 ZN.3: 4 residues within 4Å: Chain A: C.198, C.201, C.220, C.223 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.198, A:C.201, A:C.220, A:C.223 ZN.4: 4 residues within 4Å: Chain A: C.213, H.217, C.249, C.253 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.213, A:H.217, A:C.249, A:C.253 ZN.5: 4 residues within 4Å: Chain A: C.292, C.297, C.312, C.320 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.292, A:C.312, A:C.320 ZN.6: 5 residues within 4Å: Chain A: C.325, D.327, C.328, H.333, C.337 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.325, A:C.328, A:C.337 ZN.7: 4 residues within 4Å: Chain A: C.378, C.381, C.396, C.401 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.378, A:C.381, A:C.396, A:C.401 ZN.8: 4 residues within 4Å: Chain A: C.406, C.409, C.417, H.421 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.406, A:C.409, A:C.417, A:H.421

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 3 residues within 4Å: Chain A: R.265, Y.272, Q.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.272 Salt bridges: A:R.265 SO4.10: 4 residues within 4Å: Chain A: K.121, R.123, K.171, D.179 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.179 Salt bridges: A:K.121, A:R.123, A:K.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauve, V. et al., A Ubl/ubiquitin switch in the activation of Parkin. Embo J. (2015)

Release Date

2015-08-19

Peptides

E3 ubiquitin-protein ligase parkin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E3 ubiquitin-protein ligase parkin

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