6bg5

Structure of 1-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-propylpiperidin-4-yl)-3-(3-(trifluoromethyl)phenyl)urea bound to DCN1

Method: X-RAY DIFFRACTION Dmax: 85.2 Å Quality: GOOD

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

Endolysin, DCN1-like protein 1 chimera

Homo sapiens

UniProt P00720

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 Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–164 Fragment:PONY DQD N-[(2H-1,3-benzodioxol-5-yl)methyl]-N-(1-propylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;277 K;6% PEG3350, 0.2M NH4Br Resolution 1.10 Å R-free 0.172

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.

721 other PDB entries and 846 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENLYS_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 23–186; UniProt 1–164

Endolysin, DCN1-like protein 1 chimera

Homo sapiens

UniProt Q96GG9

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 Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 62–259 Fragment:PONY DQD N-[(2H-1,3-benzodioxol-5-yl)methyl]-N-(1-propylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;277 K;6% PEG3350, 0.2M NH4Br Resolution 1.10 Å R-free 0.172

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 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DCNL1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 187–384; UniProt 62–259

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 6bg5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6bg5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6bg5
Deposition date deposition_date2017-10-27
Structure title titleStructure of 1-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-propylpiperidin-4-yl)-3-(3-(trifluoromethyl)phenyl)urea bound to DCN1
Keywords keywordsE3 Ligase, HYDROLASE, LIGASE-INHIBITOR complex; HYDROLASE, LIGASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.43
Radius of gyration Rg (electron density) rg_electron24.69
Forward intensity I(0) i029730700.00
Molecular weight molecular_weight42446.0 kDa
Excluded volume excluded_volume53340 ų
Envelope volume envelope_volume65366 ų
Hydration-shell volume shell_volume23164 ų
Envelope diameter envelope_diameter85.2
Shell Rg shell_rg30.50
Envelope Rg envelope_rg24.59
Shape Rg shape_rg24.70
Total Rg total_rg25.35
Total atoms total_atoms5906
Residues n_residues366
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 dmax85.2
Rg (real space) rg_real25.51
Rg uncertainty (real space) rg_real_error0.69
I(0) (real space) i0_real2.9730e+07
I(0) uncertainty (real space) i0_real_error4.5080e+05
Rg (reciprocal space) rg_reciprocal25.49
I(0) (reciprocal space) i0_reciprocal29730000.0000
Solution quality estimate total_estimate0.8777
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary27.5
Skewness Skewness skewness0.455
Kurtosis Kurtosis kurtosis-0.219
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5831000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.916

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6bg5A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id6bg5A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily200 — Cullin, PONY binding domain

8. Citations (1)

9. Files and Curves (10)