8IKT

Ternary trans-complex of phospho-parkin with cis ACT and pUb

• PDB DOI: https://doi.org/10.2210/pdb8IKT/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-03-01 Released: 2024-09-11 
• Deposition Author(s): Lenka, D.R., Kumar, A.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.236 
• R-Value Work: 0.212 

Starting Model: experimental

Literature

Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans

Lenka, D., Dahe, S., Antico, O., Sahoo, P., Prescott, A.R., Muqit, M.M.K., Kumar, A.

(2024) Elife 

• DOI: https://doi.org/10.7554/elife.96699.2

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52.31 kDa 
• Atom Count: 3,088 
• Modelled Residue Count: 386 
• Deposited Residue Count: 463 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase parkin	A	312	Homo sapiens	Mutation(s): 1  Gene Names: PRKN, PARK2 EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for O60260 (Homo sapiens) Explore O60260  Go to UniProtKB:  O60260
PHAROS:  O60260 GTEx:  ENSG00000185345

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	75	Homo sapiens	Mutation(s): 0  Gene Names: UBA52, UBCEP2
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens) Explore P62987  Go to UniProtKB:  P62987
PHAROS:  P62987 GTEx:  ENSG00000221983

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase parkin	C	76	Homo sapiens	Mutation(s): 0  Gene Names: PRKN, PARK2 EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for O60260 (Homo sapiens) Explore O60260  Go to UniProtKB:  O60260
PHAROS:  O60260 GTEx:  ENSG00000185345

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD (Subject of Investigation/LOI)	K [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL (Subject of Investigation/LOI)	J [auth A], M [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
3CN (Subject of Investigation/LOI)	L [auth B]	3-AMINOPROPANE C3 H9 N WGYKZJWCGVVSQN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.236 
• R-Value Work: 0.212 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.764	α = 90
b = 82.764	β = 90
c = 103.494	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Lenka, D.R., Kumar, A.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	Innovative Young Biotechnology Award (DBT/12/IYBAl2019/03) and Ramalingaswami Fellowship (DBT/RLF/Re-entry/42/2019)

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release