SMTL ID : 6glc.1

Structure of phospho-Parkin bound to phospho-ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.255, H.259, C.291, C.295 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.255, A:H.259, A:C.291, A:C.295 ZN.2: 4 residues within 4Å: Chain A: C.367, C.370, H.375, C.379 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.367, A:C.370, A:H.375, A:C.379 ZN.3: 5 residues within 4Å: Chain A: C.168, T.170, C.171, C.198, C.203 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.168, A:C.171, A:C.198, A:C.203 ZN.4: 6 residues within 4Å: Chain A: C.240, T.242, C.243, R.247, C.262, C.265 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.240, A:C.243, A:C.262, A:C.265 ZN.5: 4 residues within 4Å: Chain A: C.334, C.339, C.354, C.362 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.334, A:C.339, A:C.354, A:C.362 ZN.6: 4 residues within 4Å: Chain A: C.152, C.156, C.214, H.217 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.152, A:C.156, A:C.214, A:H.217

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: P.16, E.18 No protein-ligand interaction detected (PLIP) GOL.8: 2 residues within 4Å: Chain A: P.16, R.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.16 GOL.9: 4 residues within 4Å: Chain A: F.6, G.14, I.68, S.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.14 Water bridges: A:T.219

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.10: 8 residues within 4Å: Chain A: K.301, E.302, L.303, H.304 Chain B: F.45, D.58, Y.59, N.60 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.45, B:Y.59, A:L.303 Hydrogen bonds: A:K.301, A:L.303

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

SO4.11: 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

Gladkova, C. et al., Mechanism of parkin activation by PINK1. Nature (2018)

Release Date

2018-06-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E3 ubiquitin-protein ligase parkin

Polyubiquitin-B

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