5C23: Parkin

Name: PDB 5C23: Parkin (S65DUblR0RBR)
Published: 2015-07-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Parkin (S65DUblR0RBR). Determined by X-ray diffraction at 2.37 Å resolution. Released 29 Jul 2015.

Method: X-ray diffraction
Resolution: 2.37 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,424
Mol. weight: 93.04 kDa
Ligands: ZN
Released: 29 Jul 2015

Explore 5C23 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C23 contains 29 α-helices and 74 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: 15 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	12	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	48-50	3	1
α-helix	51	1
β-strand	55	1	2
α-helix	56-59	4
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	1
β-strand	237	1	8
α-helix	238	1
β-strand	244	1	8
β-strand	248-250	3	7
β-strand	257	1	9
β-strand	258-260	3	7
α-helix	261-274	14
α-helix	277	1
β-strand	278-280	3	10
β-strand	284-286	3	10
α-helix	301-307	7
α-helix	309-327	19
β-strand	330-331	2	11
β-strand	340-341	2	11
β-strand	349-351	3	12
β-strand	363-365	3	12
β-strand	371	1	12
α-helix	377-378	2
α-helix	395-400	6
β-strand	402	1	9
β-strand	416-417	2	13
β-strand	424-425	2	13
β-strand	431	1	14
β-strand	433-435	3	15
β-strand	444-446	3	15
β-strand	452	1	15
α-helix	455-461	7
β-strand	463	1	14

Chain B: 14 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	16
α-helix	12	1
β-strand	13-16	4	16
β-strand	22	1	17
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	16
β-strand	48-50	3	16
α-helix	51	1
β-strand	55	1	17
β-strand	66-71	6	16
β-strand	147-150	4	18
β-strand	156-159	4	18
β-strand	160-166	7	19
β-strand	174-176	3	20
α-helix	183-187	5
β-strand	193	1	21
β-strand	194-196	3	20
β-strand	205	1	21
β-strand	206-212	7	19
β-strand	224-225	2	18
β-strand	229-230	2	22
α-helix	236	1
β-strand	237	1	23
α-helix	238	1
β-strand	244	1	23
β-strand	248-250	3	22
β-strand	257	1	24
β-strand	258-260	3	22
α-helix	261-274	14
α-helix	277	1
β-strand	278-280	3	25
β-strand	284-286	3	25
α-helix	301-307	7
α-helix	309-327	19
β-strand	330-331	2	26
β-strand	340-341	2	26
β-strand	349-351	3	27
β-strand	363-365	3	27
β-strand	371	1	27
α-helix	377-378	2
α-helix	395-400	6
β-strand	402	1	24
β-strand	415-417	3	28
β-strand	424-426	3	28
β-strand	431	1	29
β-strand	433-435	3	30
β-strand	444-446	3	30
β-strand	452	1	30
α-helix	455-461	7
β-strand	463	1	29

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>5C23_1 E3 ubiquitin-protein ligase parkin (chains A, B)
MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCD
LDQQDIVHIVQRPWRKGQEMNATNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGP
SCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCIT
CTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKE
LHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGC
GFAFCRECKEAYHEGECSAVFEASGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPR
CHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	16

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

Primary citation

Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis. Kumar, A., Aguirre, J.D., Condos, T.E. et al. EMBO J (2015) 34:2506-2521. DOI 10.15252/embj.201592337 · 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
5N38 2.6 Å, S65DParkin and pUB complex
8IKT 2.6 Å, Ternary trans-complex of phospho-parkin with cis ACT and pUb

Browse structure collections

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