4BM9: Autoinhibited Parkin catalytic domain

Name: PDB 4BM9: Structure of the autoinhibited Parkin catalytic domain
Published: 2013-06-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of the autoinhibited Parkin catalytic domain. Determined by X-ray diffraction at 2.25 Å resolution. Released 12 Jun 2013.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 2,398
Mol. weight: 37.72 kDa
Ligands: ZN
Released: 12 Jun 2013

Explore 4BM9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BM9 contains 12 α-helices and 29 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: 12 helices, 29 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
β-strand	223	1	2
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	258-260	3	5
α-helix	261-273	13
α-helix	277	1
β-strand	278-280	3	7
β-strand	284-286	3	7
α-helix	301-307	7
α-helix	309-316	8
α-helix	318-326	9
β-strand	330-331	2	8
β-strand	340-341	2	8
β-strand	349-351	3	9
β-strand	363-365	3	9
β-strand	371	1	9
α-helix	379-381	3
α-helix	395-400	6
β-strand	415-417	3	10
β-strand	424-426	3	10
β-strand	431	1	11
β-strand	433-435	3	12
β-strand	444-446	3	12
β-strand	452	1	12
α-helix	453	1
α-helix	455-461	7
β-strand	463	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase parkin	A	protein	329	HOMO SAPIENS	O60260 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4BM9_1 E3 UBIQUITIN-PROTEIN LIGASE PARKIN (chains A)
PAGRSIYNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGEC
QSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSR
HVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQ
QYGAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHEGE
CSAVFEASGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMHMKC
PQPQCRLEWCWNCGCEWNRVCMGDHWFDV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

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

Primary citation

Structure of the Human Parkin Ligase Domain in an Autoinhibited State. Wauer, T., Komander, D. EMBO J (2013) 32:2099. DOI 10.1038/EMBOJ.2013.125 · 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
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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