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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：Q9JK66 New Search
5PDB entries
19Biological assembly
19chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
2KNB Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain Deposited 2009-08-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 1.2 mM [U-99% 13C; U-99% 15N] Ubl, 1.2 mM SH3, 100% D2O | 100% D2O
NMR sample composition 1.2 mM [U-99% 13C; U-99% 15N] SH3, 1.2 mM Ubl, 100% D2O | 100% D2O
NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] Ubl, 1.6 mM SH3, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] SH3, 1.6 mM Ubl, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.8 mM [U-99% 15N] Ubl, 1.6 mM SH3, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.8 mM [U-99% 15N] SH3, 1.6 mM Ubl, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
4K7D Crystal Structure of Parkin C-terminal RING domains Deposited 2013-04-17 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 141–465（325 aa） Fragment：C-terminal RING domains (141-465)
Not recorded ZN ZINC ION × 8 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.9 M sodium malonate pH 7.0, 0.1 M HEPES pH 7.0, 5% (v/v) glycerol, 56 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.233
4K7D Crystal Structure of Parkin C-terminal RING domains Deposited 2013-04-17 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 141–465（325 aa） Fragment：C-terminal RING domains (141-465)
Not recorded ZN ZINC ION × 8 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.9 M sodium malonate pH 7.0, 0.1 M HEPES pH 7.0, 5% (v/v) glycerol, 56 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.233
4K7D Crystal Structure of Parkin C-terminal RING domains Deposited 2013-04-17 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 141–465（325 aa） Fragment：C-terminal RING domains (141-465)
Not recorded ZN ZINC ION × 8 MLI MALONATE ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.9 M sodium malonate pH 7.0, 0.1 M HEPES pH 7.0, 5% (v/v) glycerol, 56 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.233
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain J 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain K 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain L 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain D 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain E 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain F 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain G 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain H 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4K95 Crystal Structure of Parkin Deposited 2013-04-19 Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain I 1–465（465 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Resolution 6.50 Å R-free 0.327
4ZYN Crystal Structure of Parkin E3 ubiquitin ligase (linker deletion; delta 86-130) Deposited 2015-05-21 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–465（465 aa）
Not recorded ZN ZINC ION × 8 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.3M Ammonium Sulfate, 0.1M HEPES pH 7.5, 18% (w/v) PEG 3350
Resolution 2.54 Å R-free 0.235
4ZYN Crystal Structure of Parkin E3 ubiquitin ligase (linker deletion; delta 86-130) Deposited 2015-05-21 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–465（465 aa）
Not recorded ZN ZINC ION × 8 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.3M Ammonium Sulfate, 0.1M HEPES pH 7.5, 18% (w/v) PEG 3350
Resolution 2.54 Å R-free 0.235
8W31 Crystal structure of parkin (R0RB):2pUb with activator compound Deposited 2024-02-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 145–379（235 aa） Fragment：residues 145-379
Not recorded ZN ZINC ION × 6 A1AE9 (S)-1-(6-benzyl-3-(4-(1,2,3,4-tetrahydroquinoline-1-carbonyl)phenyl)-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl)ethan-1-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M Sodium Chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350
Resolution 2.50 Å R-free 0.294

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.