5c23

Parkin (S65DUblR0RBR)

Method: X-RAY DIFFRACTION Dmax: 104.3 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase parkin

Homo sapiens

UniProt O60260

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.

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

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5c23

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5c23
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5c23
Deposition date deposition_date2015-06-15
Structure title titleParkin (S65DUblR0RBR)
Keywords keywordsE3 ligase2, ligase; LIGASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.14
Radius of gyration Rg (electron density) rg_electron32.31
Forward intensity I(0) i0144616000.00
Molecular weight molecular_weight88351.0 kDa
Excluded volume excluded_volume107300 ų
Envelope volume envelope_volume150240 ų
Hydration-shell volume shell_volume39356 ų
Envelope diameter envelope_diameter110.9
Shell Rg shell_rg38.69
Envelope Rg envelope_rg31.95
Shape Rg shape_rg32.28
Total Rg total_rg32.89
Total atoms total_atoms6098
Residues n_residues768
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax104.3
Rg (real space) rg_real33.02
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real1.4460e+08
I(0) uncertainty (real space) i0_real_error2.2880e+06
Rg (reciprocal space) rg_reciprocal33.08
I(0) (reciprocal space) i0_reciprocal144600000.0000
Solution quality estimate total_estimate0.6867
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.3
Skewness Skewness skewness0.184
Kurtosis Kurtosis kurtosis-0.523
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10930000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 0.049; Positv: 1.000; Valcen: 1.000; Smooth: 0.904

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5c23A01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id5c23B01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

8. Citations (1)

9. Files and Curves (10)