4I1F: Parkin-S223P E3 ligase

Name: PDB 4I1F: Structure of Parkin-S223P E3 ligase
Published: 2013-06-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of Parkin-S223P E3 ligase. Determined by X-ray diffraction at 1.58 Å resolution. Released 19 Jun 2013.

Method: X-ray diffraction
Resolution: 1.58 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,679
Mol. weight: 37.11 kDa
Ligands: ZN, BA
Released: 19 Jun 2013

Explore 4I1F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4I1F contains 9 α-helices and 30 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: 9 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	147-150	4	1
β-strand	156-159	4	1
β-strand	160-166	7	2
β-strand	174-176	3	3
α-helix	183-187	5
β-strand	193	1	4
β-strand	194-196	3	3
β-strand	205	1	4
β-strand	206-212	7	2
α-helix	223	1
β-strand	224-225	2	1
β-strand	229-230	2	5
α-helix	236	1
β-strand	237	1	6
α-helix	238	1
β-strand	244	1	6
β-strand	248-250	3	5
β-strand	257	1	7
β-strand	258-260	3	5
α-helix	261-273	13
β-strand	278-280	3	8
β-strand	284-286	3	8
α-helix	301-307	7
α-helix	309-326	18
β-strand	330-331	2	9
β-strand	340-341	2	9
β-strand	349-351	3	10
β-strand	363-365	3	10
β-strand	371	1	10
α-helix	395-400	6
β-strand	402	1	7
β-strand	415-417	3	11
β-strand	424-426	3	11
β-strand	431	1	12
β-strand	433-435	3	13
β-strand	444-446	3	13
β-strand	452	1	13
α-helix	455-461	7
β-strand	463	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase parkin	A	protein	325	Homo sapiens	O60260 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4I1F_1 E3 ubiquitin-protein ligase parkin (chains A)
SIYNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPH
CPGTSAEFFFKCGAHPTSDKETPVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVIC
LDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGA
EECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAV
FEASGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMHMKCPQPQ
CRLEWCWNCGCEWNRVCMGDHWFDV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
BA	Barium ion	Ba	1

Primary citation

Structure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases. Riley, B.E., Lougheed, J.C., Callaway, K. et al. Nat Commun (2013) 4:1982-1982. DOI 10.1038/ncomms2982 · PubMed

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

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
8IKT 2.6 Å, Ternary trans-complex of phospho-parkin with cis ACT and pUb

Browse structure collections

About this viewer

MolViewer shows 4I1F directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.