SMTL ID : 7us1.1

Structure of parkin (R0RB) bound to two phospho-ubiquitin molecules

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

hetero-1-2-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.114, H.118, C.150, C.154 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.114, A:H.118, A:C.150, A:C.154 ZN.2: 4 residues within 4Å: Chain A: C.226, C.229, H.234, C.238 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.226, A:C.229, A:H.234, A:C.238 ZN.3: 5 residues within 4Å: Chain A: C.27, T.29, 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.4: 4 residues within 4Å: Chain A: C.99, C.102, C.121, C.124 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.99, A:C.102, A:C.121, A:C.124 ZN.5: 4 residues within 4Å: Chain A: C.193, C.198, C.213, C.221 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.193, A:C.198, A:C.213, A:C.221 ZN.6: 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

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 5 residues within 4Å: Chain A: Y.10, H.16, V.18, L.122, I.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.10, A:V.18

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 7 residues within 4Å: Chain A: N.88, L.89, Q.113, L.158, I.159, K.160, E.161 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.88, A:L.158, A:K.160, A:E.161 EDO.9: 6 residues within 4Å: Chain A: K.160, E.161, L.162, H.163 Chain B: K.48, Y.59 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.48, A:E.161, A:L.162 EDO.10: 4 residues within 4Å: Chain B: L.15, E.16, K.29, K.33 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.16, B:K.33 EDO.11: 4 residues within 4Å: Chain C: L.15, E.16, K.29, K.33 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.16, C:K.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fakih, R. et al., Structure of the second phosphoubiquitin-binding site in parkin. J.Biol.Chem. (2022)

Release Date

2022-06-22

Peptides

E3 ubiquitin-protein ligase parkin: A
Ubiquitin-G76 deletion: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E3 ubiquitin-protein ligase parkin

Ubiquitin-G76 deletion

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