5TR5: Serine 65 phosphorylated UBL domain from parkin

Solution structure of Serine 65 phosphorylated UBL domain from parkin. Determined by solution NMR. Released 21 Dec 2016.

Method: Solution NMR
Organism: Homo sapiens
Chains: 1
Atoms: 627
Mol. weight: 8.92 kDa
Released: 21 Dec 2016

Explore 5TR5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TR5 contains 3 α-helices and 8 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-44	4	1
β-strand	45	1	3
β-strand	48	1	3
α-helix	49-51	3
β-strand	55	1	2
β-strand	67-71	5	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase parkin	A	protein	76	Homo sapiens	O60260 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5TR5_1 E3 ubiquitin-protein ligase parkin (chains A)
MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCD
LDQQSIVHIVQRPWRK

Primary citation

Structure of phosphorylated UBL domain and insights into PINK1-orchestrated parkin activation. Aguirre, J.D., Dunkerley, K.M., Mercier, P. et al. Proc Natl Acad Sci U S A (2017) 114:298-303. DOI 10.1073/pnas.1613040114 · PubMed

Other PDB entries of the same protein (UniProt O60260 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4I1F 1.58 Å, Structure of Parkin-S223P E3 ligase
5C1Z 1.79 Å, Parkin (UblR0RBR)
6GLC 1.8 Å, Structure of phospho-Parkin bound to phospho-ubiquitin
8WZN 1.8 Å, ParkinK211N in complex with phospho NEDD8
8IKM 1.92 Å, Trans complex of phospho parkin
4I1H 2.0 Å, Structure of Parkin E3 ligase
4BM9 2.25 Å, Structure of the autoinhibited Parkin catalytic domain
8WZO 2.25 Å, Parkin in complex with phospho NEDD8
5C9V 2.35 Å, Structure of human Parkin G319A
8IKV 2.35 Å, pUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb
5C23 2.37 Å, Parkin (S65DUblR0RBR)
5N38 2.6 Å, S65DParkin and pUB complex

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