6GLC: Phospho-Parkin

Structure of phospho-Parkin bound to phospho-ubiquitin. Determined by X-ray diffraction at 1.8 Å resolution. Released 13 Jun 2018.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,245
Mol. weight: 52.53 kDa
Ligands: ZN
Released: 13 Jun 2018

Explore 6GLC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GLC contains 17 α-helices and 32 β-strands across 2 chains. 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: 12 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	1
α-helix	10-12	3
β-strand	13-17	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-50	3	1
α-helix	51	1
β-strand	55	1	2
α-helix	57-59	3
α-helix	61-62	2
β-strand	66-71	6	1
α-helix	102-104	3
β-strand	146-150	5	3
β-strand	156-166	11	3
β-strand	174-176	3	4
α-helix	183-187	5
β-strand	193	1	5
β-strand	194-196	3	4
β-strand	205	1	5
β-strand	206-212	7	3
β-strand	224-225	2	3
β-strand	229-230	2	6
α-helix	236-238	3
β-strand	248-250	3	6
β-strand	258-260	3	6
α-helix	261-273	13
β-strand	278-280	3	7
β-strand	284-286	3	7
α-helix	301-307	7
α-helix	309-326	18
β-strand	330-331	2	8
β-strand	340-342	3	8
β-strand	349-351	3	9
β-strand	363-365	3	9
β-strand	371	1	9

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	8
β-strand	12-16	5	8
β-strand	22	1	10
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	8
β-strand	48-49	2	8
α-helix	50-51	2
β-strand	55	1	10
α-helix	57-59	3
α-helix	61-62	2
β-strand	66-72	7	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase parkin	A	protein	389	Homo sapiens	O60260 (AlphaFold model)
Polyubiquitin-B	B	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6GLC_1 E3 ubiquitin-protein ligase parkin (chains A)
GPMIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQN
CDLDQQSIVHIVQRPWRKGQEMNATGGDDPRNAAGGCEREPQSLTRVDLSSSVLPGDSVG
LAVILHTDSRKDSPPAGSPAGRSIYNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQ
GPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITC
ITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLI
KELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDCRKVTCEGGNGL
GCGFAFCRECKEAYHEGECSAVFENLYFQ

Sequence of entity 2 (B), FASTA

>6GLC_2 Polyubiquitin-B (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Water and common crystallization additives (GOL, MPD, SO4) are not listed.

Primary citation

Mechanism of parkin activation by PINK1. Gladkova, C., Maslen, S.L., Skehel, J.M. et al. Nature (2018) 559:410-414. DOI 10.1038/s41586-018-0224-x · 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)
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
8IKT 2.6 Å, Ternary trans-complex of phospho-parkin with cis ACT and pUb

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