9f19

Human USP30 chimera in complex with NK036 inhibitor

Method: X-RAY DIFFRACTION Dmax: 83.6 Å Quality: GOOD

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

Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin carboxyl-terminal hydrolase 35

Homo sapiens

UniProt P54578

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 248–272 Chain A; UniProt 295–320 Chain B; UniProt 248–272 Chain B; UniProt 295–320 Not recorded A1H8X 4-fluoranyl-~{N}-[(2~{S})-1-[[4-[(2-methyl-1-oxidanyl-propan-2-yl)sulfamoyl]phenyl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]benzamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;76 mM NaOH, 100 mM Bicine, 10.2% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM L-Proline (Crystal 1) X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;85 mM NaOH, 100 mM Bicine, 10.2% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM L-Proline (Crystal 2) X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;88 mM NaOH, 100 mM Bicine, 11% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM Sarcosine (Crystal 3) Resolution 2.75 Å R-free 0.266

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.

22 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBP14_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 130–154; UniProt 248–272 Author chain A; PDBConstruct 182–207; UniProt 295–320 Author chain B; PDBConstruct 130–154; UniProt 248–272 Author chain B; PDBConstruct 182–207; UniProt 295–320

Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin carboxyl-terminal hydrolase 35

Homo sapiens

UniProt Q70CQ3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 64–178 Chain A; UniProt 217–224 Chain A; UniProt 249–275 Chain A; UniProt 318–348 Chain A; UniProt 437–502 Chain B; UniProt 64–178 Chain B; UniProt 217–224 Chain B; UniProt 249–275 Chain B; UniProt 318–348 Chain B; UniProt 437–502 Not recorded A1H8X 4-fluoranyl-~{N}-[(2~{S})-1-[[4-[(2-methyl-1-oxidanyl-propan-2-yl)sulfamoyl]phenyl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]benzamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;76 mM NaOH, 100 mM Bicine, 10.2% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM L-Proline (Crystal 1) X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;85 mM NaOH, 100 mM Bicine, 10.2% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM L-Proline (Crystal 2) X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;88 mM NaOH, 100 mM Bicine, 11% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM Sarcosine (Crystal 3) Resolution 2.75 Å R-free 0.266

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.

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBP30_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–117; UniProt 64–178 Author chain A; PDBConstruct 122–129; UniProt 217–224 Author chain A; PDBConstruct 155–181; UniProt 249–275 Author chain A; PDBConstruct 208–238; UniProt 318–348 Author chain A; PDBConstruct 252–317; UniProt 437–502 Author chain B; PDBConstruct 3–117; UniProt 64–178 Author chain B; PDBConstruct 122–129; UniProt 217–224 Author chain B; PDBConstruct 155–181; UniProt 249–275 Author chain B; PDBConstruct 208–238; UniProt 318–348 Author chain B; PDBConstruct 252–317; UniProt 437–502

Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin carboxyl-terminal hydrolase 35

Homo sapiens

UniProt Q9P2H5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 833–845 Chain B; UniProt 833–845 Not recorded A1H8X 4-fluoranyl-~{N}-[(2~{S})-1-[[4-[(2-methyl-1-oxidanyl-propan-2-yl)sulfamoyl]phenyl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]benzamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;76 mM NaOH, 100 mM Bicine, 10.2% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM L-Proline (Crystal 1) X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;85 mM NaOH, 100 mM Bicine, 10.2% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM L-Proline (Crystal 2) X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;88 mM NaOH, 100 mM Bicine, 11% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM Sarcosine (Crystal 3) Resolution 2.75 Å R-free 0.266

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.

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBP35_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 239–251; UniProt 833–845 Author chain B; PDBConstruct 239–251; UniProt 833–845

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 9f19

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9f19
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9f19
Deposition date deposition_date2024-04-18
Structure title titleHuman USP30 chimera in complex with NK036 inhibitor
Keywords keywords;USP30, Ubiquitin, inhibitor, DUB, deubiquitinating enzyme, USP14, USP35, mitophagy, USP, Ubiquitin-specific protease, Ubiquitin carboxyl-terminal hydrolase 30, Compound 39, Sulfonamide, Phenylalanine, HYDROLASE ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.90
Radius of gyration Rg (electron density) rg_electron25.23
Forward intensity I(0) i093457500.00
Molecular weight molecular_weight50961.0 kDa
Excluded volume excluded_volume49431 ų
Envelope volume envelope_volume85925 ų
Hydration-shell volume shell_volume28711 ų
Envelope diameter envelope_diameter85.2
Shell Rg shell_rg32.21
Envelope Rg envelope_rg25.08
Shape Rg shape_rg25.21
Total Rg total_rg25.83
Total atoms total_atoms3863
Residues n_residues503
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 dmax83.6
Rg (real space) rg_real25.91
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real9.3460e+07
I(0) uncertainty (real space) i0_real_error1.4630e+06
Rg (reciprocal space) rg_reciprocal25.91
I(0) (reciprocal space) i0_reciprocal93460000.0000
Solution quality estimate total_estimate0.8915
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.8
Skewness Skewness skewness0.373
Kurtosis Kurtosis kurtosis-0.380
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15240000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.927

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)