SMTL ID : 5caw.2 (1 other biounit)

Structure of Pediculus humanus Parkin bound to phospho-ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

hetero-1-1-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.11, C.15, C.73, H.76 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.11, A:C.15, A:C.73, A:H.76 ZN.2: 4 residues within 4Å: Chain A: C.27, C.30, C.57, C.62 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.27, A:C.30, A:C.57, A:C.62 ZN.3: 4 residues within 4Å: Chain A: C.100, C.103, C.122, C.125 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.100, A:C.103, A:C.122, A:C.125 ZN.4: 4 residues within 4Å: Chain A: C.115, H.119, C.151, C.155 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.115, A:H.119, A:C.151, A:C.155 ZN.5: 4 residues within 4Å: Chain A: C.194, C.199, C.214, C.216 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.194, A:C.199, A:C.214, A:C.216 ZN.6: 4 residues within 4Å: Chain A: C.221, C.224, H.229, C.233 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.221, A:C.224, A:H.229, A:C.233 ZN.7: 4 residues within 4Å: Chain A: C.275, C.278, C.293, C.298 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.275, A:C.278, A:C.293, A:C.298 ZN.8: 4 residues within 4Å: Chain A: C.303, C.306, C.314, H.318 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.303, A:C.306, A:C.314, A:H.318

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

SO4.9: 4 residues within 4Å: Chain A: S.43, W.44, K.92, R.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.44 Salt bridges: A:K.92, A:R.118 SO4.10: 6 residues within 4Å: Chain A: G.55, V.56, C.57, C.62, E.63, G.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.57, A:C.62 SO4.11: 2 residues within 4Å: Chain A: T.170, D.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.171 SO4.12: 3 residues within 4Å: Chain B: R.42, R.72, R.74 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.42, B:R.72, B:R.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wauer, T. et al., Mechanism of phospho-ubiquitin-induced PARKIN activation. Nature (2015)

Release Date

2015-07-22

Peptides

E3 ubiquitin-protein ligase parkin: A
Polyubiquitin-B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

E3 ubiquitin-protein ligase parkin

Polyubiquitin-B

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