5N2W: WT-Parkin and pUB complex

Name: PDB 5N2W: WT-Parkin and pUB complex
Published: 2017-04-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

WT-Parkin and pUB complex. Determined by X-ray diffraction at 2.68 Å resolution. Released 19 Apr 2017.

Method: X-ray diffraction
Resolution: 2.68 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,681
Mol. weight: 54.95 kDa
Ligands: TMO, ZN
Released: 19 Apr 2017

Explore 5N2W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5N2W contains 14 α-helices and 42 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: 11 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	13-16	4	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
β-strand	66-71	6	1
β-strand	147-150	4	3
β-strand	156-159	4	3
β-strand	160-166	7	4
β-strand	174-176	3	5
α-helix	183-187	5
β-strand	193	1	6
β-strand	194-196	3	5
β-strand	205	1	6
β-strand	206-212	7	4
β-strand	224-225	2	3
β-strand	229-230	2	7
α-helix	236-238	3
β-strand	248-250	3	7
β-strand	257	1	8
β-strand	258-260	3	7
α-helix	261-273	13
β-strand	278-280	3	9
β-strand	284-286	3	9
α-helix	301-307	7
α-helix	309-326	18
β-strand	330-331	2	10
β-strand	340-342	3	10
β-strand	349-351	3	11
β-strand	363-365	3	11
β-strand	371	1	11
α-helix	388-390	3
α-helix	395-400	6
β-strand	402	1	8
β-strand	415-417	3	12
β-strand	424-426	3	12
β-strand	431	1	13
β-strand	433-435	3	14
β-strand	444-446	3	14
β-strand	452	1	14
α-helix	455-461	7
β-strand	463	1	13

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	10
β-strand	12-16	5	10
β-strand	22	1	15
α-helix	23-34	12
β-strand	41-45	5	10
β-strand	48-49	2	10
α-helix	50-51	2
β-strand	55	1	15
α-helix	57-59	3
β-strand	66-72	7	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase parkin,E3 ubiquitin-protein ligase parkin	A	protein	405	Homo sapiens	O60260 (AlphaFold model)
Polyubiquitin-B	B	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5N2W_1 E3 ubiquitin-protein ligase parkin,E3 ubiquitin-protein ligase parkin (chains A)
MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCD
LDQQSIVHIVQRPWRKGQEMNATNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGP
SCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCIT
CTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKE
LHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDCRKVTCEGGNGLGC
GFAFCRECKEAYHEGECSAVFEASGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPR
CHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV

Sequence of entity 2 (B), FASTA

>5N2W_2 Polyubiquitin-B (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGX

Ligands and cofactors

ID	Name	Formula	Copies
TMO	trimethylamine oxide	C3 H9 N O	2
ZN	Zinc ion	Zn	8

Water and common crystallization additives (CL) are not listed.

Primary citation

Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity. Kumar, A., Chaugule, V.K., Condos, T.E.C. et al. Nat Struct Mol Biol (2017) 24:475-483. DOI 10.1038/nsmb.3400 · 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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