SMTL ID : 5c9v.1

Structure of human Parkin G319A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.15, C.19, C.77, H.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.15, A:C.19, A:C.77, A:H.80 ZN.2: 4 residues within 4Å: Chain A: C.118, H.122, C.154, C.158 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.118, A:H.122, A:C.154, A:C.158 ZN.3: 4 residues within 4Å: Chain A: C.311, C.314, C.322, H.326 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.311, A:C.314, A:C.322, A:H.326 ZN.4: 5 residues within 4Å: Chain A: C.31, C.34, C.61, S.63, C.66 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.31, A:C.34, A:C.61, A:C.66 ZN.5: 4 residues within 4Å: Chain A: C.103, C.106, C.125, C.128 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.103, A:C.106, A:C.125, A:C.128 ZN.6: 4 residues within 4Å: Chain A: C.197, C.202, C.217, C.225 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.197, A:C.202, A:C.217, A:C.225 ZN.7: 5 residues within 4Å: Chain A: C.230, C.233, H.238, C.242 Ligands: GOL.15 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.230, A:C.233, A:H.238, A:C.242 ZN.8: 4 residues within 4Å: Chain A: C.283, C.286, C.301, C.306 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.283, A:C.286, A:C.301, A:C.306

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

SO4.9: 3 residues within 4Å: Chain A: R.28, K.76, T.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.82 Salt bridges: A:R.28, A:K.76 SO4.10: 2 residues within 4Å: Chain A: N.319, R.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.320 Salt bridges: A:R.320 SO4.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.12: 2 residues within 4Å: Chain A: N.119, P.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.119 SO4.13: 4 residues within 4Å: Chain A: K.16, H.167, R.170, Y.177 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.16, A:H.167, A:R.170 SO4.14: 2 residues within 4Å: Chain A: R.213, Y.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.237 Salt bridges: A:R.213

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 6 residues within 4Å: Chain A: C.233, H.238, E.241, C.242, S.243 Ligands: ZN.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.243 GOL.16: 5 residues within 4Å: Chain A: V.51, L.52, P.54, E.72, F.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.51, A:F.73 Water bridges: A:N.55, A:N.55 GOL.17: 3 residues within 4Å: Chain A: N.160, S.161, L.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.160, A:S.161, A:L.162

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase parkin