E3 ubiquitin-protein ligase parkin
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count | Chain A; UniProt 1–465 | Not recorded | ZN ZINC ION × 8 GOL GLYCEROL × 2 SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.5;277 K;PEG3350, LiSO4 | Resolution 2.37 Å R-free 0.241 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count | Chain B; UniProt 1–465 | Not recorded | ZN ZINC ION × 8 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.5;277 K;PEG3350, LiSO4 | Resolution 2.37 Å R-free 0.241 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 5C23 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1IYF Solution structure of ubiquitin-like domain of human parkin Deposited 2002-08-13 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–76(76 aa)
Fragment:ubiquitin-like domain
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6;303 K;Ionic strength (raw mmCIF value) 0.3;Pressure 1
NMR measurement conditions
pH 6;310 K;Ionic strength (raw mmCIF value) 0.3;Pressure 1
NMR sample composition
0.1mM parkin ubiquitin-like domain U-15N, 13C; 50mM potassium phosphate buffer | 90% H2O/10% D2O
NMR sample composition
0.1mM parkin ubiquitin-like domain U-15N, 13C; 50mM potassium phosphate buffer | 90% H2O, 10% D2O, 5%-DMPC/DHPC; 90% H2O, 10% D2O, 5%-DMPC/DHPC/CTAB
|
Resolution not provided |
| 2JMO IBR domain of Human Parkin Deposited 2006-11-24 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
308–384(77 aa)
Fragment:IBR-type 1 domain, residues 308-384
|
Not recorded | ZN ZINC ION × 2 |
SOLUTION NMR
NMR measurement conditions
pH 6.95;298 K;Ionic strength (raw mmCIF value) 100 mM NaCl, 25 mM Na2HPO4;Pressure ambient
NMR sample composition
0.2 mM [U-100% 13C, U-100% 15N] IBR, 25 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.033 mM DSS, 100% D2O | 100% D2O
NMR sample composition
0.2 mM [U-100% 13C, U-100% 15N] IBR, 25 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.033 mM DSS, 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 4BM9 Structure of the autoinhibited Parkin catalytic domain Deposited 2013-05-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer;Protein × 6 PDB declaration: hexameric |
Chain A
137–465(329 aa)
Fragment:UPD AND RBR DOMAIN, RESIDUES 137-465
|
Not recorded | ZN ZINC ION × 48 SO4 SULFATE ION × 18 GOL GLYCEROL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7;1.6 M LITHIUM SULPHATE, 10 MM MAGNESIUM CHLORIDE, 50 MM MES (PH 5.4)
|
Resolution 2.25 Å R-free 0.218 |
| 4I1F Structure of Parkin-S223P E3 ligase Deposited 2012-11-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
141–465(325 aa)
Fragment:R0RBR (UNP residues 141-465)
|
Mutation:S223P | ZN ZINC ION × 8 BA BARIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;283 K;0.1 M HEPES, pH 7.5, 20% PEG4000, 10% isopropanol, 10 mM barium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 283K
|
Resolution 1.58 Å R-free 0.245 |
| 4I1H Structure of Parkin E3 ligase Deposited 2012-11-20 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
141–465(325 aa)
Fragment:R0RBR (UNP residues 141-465)
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 6.5;283 K;0.1 M Tris, pH 6.5, 0.2 M sodium chloride, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 383K
|
Resolution 2.00 Å R-free 0.215 |
| 5C1Z Parkin (UblR0RBR) Deposited 2015-06-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–465(465 aa)
|
Not recorded | ZN ZINC ION × 8 SO4 SULFATE ION × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;pH 5.5;277 K;LiSO4, PEG3350
|
Resolution 1.79 Å R-free 0.212 |
| 5C1Z Parkin (UblR0RBR) Deposited 2015-06-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
1–465(465 aa)
|
Not recorded | ZN ZINC ION × 8 SO4 SULFATE ION × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;pH 5.5;277 K;LiSO4, PEG3350
|
Resolution 1.79 Å R-free 0.212 |
| 5C9V Structure of human Parkin G319A Deposited 2015-06-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
137–465(329 aa)
Fragment:UNP residues 137-465
|
Mutation:G319A | ZN ZINC ION × 8 SO4 SULFATE ION × 6 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 5.6;291 K;1.8 M lithium sulphate, 0.01 M MgCl2, 0.05 M MES pH 5.6
|
Resolution 2.35 Å R-free 0.229 |
| 5N2W WT-Parkin and pUB complex Deposited 2017-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
1–83(83 aa)
Chain A
144–465(322 aa)
|
Not recorded | ZN ZINC ION × 8 CL CHLORIDE ION × 1 TMO trimethylamine oxide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;277 K;100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000
|
Resolution 2.68 Å R-free 0.243 |
| 5N38 S65DParkin and pUB complex Deposited 2017-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
1–83(83 aa)
Chain A
144–465(322 aa)
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;277 K;100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000
|
Resolution 2.60 Å R-free 0.236 |
| 5TR5 Solution structure of Serine 65 phosphorylated UBL domain from parkin Deposited 2016-10-25 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–76(76 aa)
Fragment:residues 1-76
|
Non-standard monomer:Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7;298 K;Ionic strength (raw mmCIF value) 100;Pressure 1
NMR sample composition
300 uM [U-15N] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
300 uM [U-13C] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
400 uM [U-99% 13C; U-99% 15N] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
400 uM pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 100% D2O | 100% D2O
|
Resolution not provided |
| 6GLC Structure of phospho-Parkin bound to phospho-ubiquitin Deposited 2018-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
1–382(382 aa)
|
Non-standard monomer:Yes (specific site not provided by mmCIF) | ZN ZINC ION × 6 GOL GLYCEROL × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.03 M of each sodium nitrate, disodium hydrogen phosphate, ammonium sulphate, 0.1 M MOPS/HEPES-Na (pH 7.5)
|
Resolution 1.80 Å R-free 0.205 |
| 6HUE ParkinS65N Deposited 2018-10-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–465(465 aa)
|
Not recorded | ZN ZINC ION × 8 SO4 SULFATE ION × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;277 K;100mM BIS-TRIS pH 5.5, 200mM LiSO4 and 20% PEG3350
|
Resolution 2.85 Å R-free 0.255 |
| 6HUE ParkinS65N Deposited 2018-10-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
1–465(465 aa)
|
Not recorded | ZN ZINC ION × 8 SO4 SULFATE ION × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;277 K;100mM BIS-TRIS pH 5.5, 200mM LiSO4 and 20% PEG3350
|
Resolution 2.85 Å R-free 0.255 |
| 6N13 UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin Deposited 2018-11-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric |
Chain B
144–465(322 aa)
|
Mutation:Q347C | ZN ZINC ION × 8 |
SOLUTION NMR
NMR measurement conditions
pH 7;298 K;Ionic strength (raw mmCIF value) 50;Pressure ambient
NMR sample composition
0.11 mM [U-13C; U-15N; U-2H] UbcH7, 0.11 mM [U-13C; U-15N; U-2H] ubiquitin, 0.11 mM [U-2H] Parkin -residues 144-465 comprising the RING0-RING1-IBR and RING2(Rcat) domains, 0.11 mM [U-2H] phosphorylated ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 8IK6 pUbl depleted Parkin complex with pUbiquitin Deposited 2023-02-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain C
139–465(327 aa)
|
Mutation:R140P,Q347C,A383N,S384L,G385Y,T386F,T387Q,T388S | ZN ZINC ION × 8 SO4 SULFATE ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;277 K;1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane
|
Resolution 3.30 Å R-free 0.270 |
| 8IK6 pUbl depleted Parkin complex with pUbiquitin Deposited 2023-02-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
139–465(327 aa)
|
Mutation:R140P,Q347C,A383N,S384L,G385Y,T386F,T387Q,T388S | ZN ZINC ION × 6 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;277 K;1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane
|
Resolution 3.30 Å R-free 0.270 |
| 8IKM Trans complex of phospho parkin Deposited 2023-02-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric |
Chain A
141–382(242 aa)
Chain C
1–140(140 aa)
|
Mutation:Q347C Non-standard monomer:Yes (specific site not provided by mmCIF) | ZN ZINC ION × 6 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;291 K;0.3 M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3 M Ammonium sulfate,1.0 M 8.5 Tris (base), BICINE, 25% v/v MPD; 25% PEG 1000, 25% w/v PEG 3350
|
Resolution 1.92 Å R-free 0.233 |
| 8IKT Ternary trans-complex of phospho-parkin with cis ACT and pUb Deposited 2023-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric |
Chain A
77–382(306 aa)
Chain C
1–76(76 aa)
|
Mutation:Q347C Non-standard monomer:Yes (specific site not provided by mmCIF) | ZN ZINC ION × 6 GOL GLYCEROL × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 3CN 3-AMINOPROPANE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;291 K;0.3 M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3 M Ammonium sulfate, Imidazole, MES monohydrate (acid), 25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350
|
Resolution 2.60 Å R-free 0.236 |
| 8IKV pUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb Deposited 2023-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain C
139–465(327 aa)
|
Mutation:R140P,R163D,K211N,Q347C | ZN ZINC ION × 8 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;291 K;0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 2.35 Å R-free 0.217 |
| 8IKV pUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb Deposited 2023-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
139–465(327 aa)
|
Mutation:R140P,R163D,K211N,Q347C | ZN ZINC ION × 8 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;291 K;0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 2.35 Å R-free 0.217 |
| 8JWV Untethered R0RBR Deposited 2023-06-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
141–465(325 aa)
|
Not recorded | ZN ZINC ION × 8 GOL GLYCEROL × 2 BA BARIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;277 K;0.1 M HEPES, pH 7.5, 8% PEG 4000, 10% isopropanol, 0.1 M BaCl2
|
Resolution 2.90 Å R-free 0.254 |
| 8WZN ParkinK211N in complex with phospho NEDD8 Deposited 2023-11-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
141–465(325 aa)
|
Mutation:K211N | ZN ZINC ION × 8 PEG DI(HYDROXYETHYL)ETHER × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;291 K;0.1 M, MMT, 7.0, 25% w/v, PEG 1500
|
Resolution 1.80 Å R-free 0.212 |
| 8WZO Parkin in complex with phospho NEDD8 Deposited 2023-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
141–465(325 aa)
|
Not recorded | ZN ZINC ION × 8 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;277 K;0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, 7.5, 20% w/v PEG 3350
|
Resolution 2.25 Å R-free 0.248 |
20 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | PRKN2_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 1–405; UniProt 1–465 Author chain B; PDBConstruct 1–405; UniProt 1–465 |