7bdh

Notum Fragment 955

Method: X-RAY DIFFRACTION Dmax: 67.6 Å Quality: GOOD

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

Palmitoleoyl-protein carboxylesterase NOTUM

Homo sapiens

UniProt Q6P988

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 81–451 Not recorded SO4 SULFATE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 DMS DIMETHYL SULFOXIDE × 1 TEZ N-(2,1,3-Benzothiadiazol-5-yl)acetamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;296 K;1.5 M Ammonium Sulphate 0.1 M Sodium Citrate, pH4.2 Resolution 1.54 Å R-free 0.217

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.

140 other PDB entries and 149 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOTUM_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–374; UniProt 81–451

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 7bdh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7bdh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7bdh
Deposition date deposition_date2020-12-21
Structure title titleNotum Fragment 955
Keywords keywordsNotum Inhibitor Fragment Screen, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.26
Radius of gyration Rg (electron density) rg_electron19.83
Forward intensity I(0) i027973000.00
Molecular weight molecular_weight39366.0 kDa
Excluded volume excluded_volume48672 ų
Envelope volume envelope_volume56910 ų
Hydration-shell volume shell_volume23273 ų
Envelope diameter envelope_diameter71.2
Shell Rg shell_rg27.08
Envelope Rg envelope_rg20.19
Shape Rg shape_rg19.78
Total Rg total_rg20.85
Total atoms total_atoms2767
Residues n_residues340
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 dmax67.6
Rg (real space) rg_real21.11
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real2.7970e+07
I(0) uncertainty (real space) i0_real_error3.0730e+05
Rg (reciprocal space) rg_reciprocal21.14
I(0) (reciprocal space) i0_reciprocal27970000.0000
Solution quality estimate total_estimate0.8937
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.8
Skewness Skewness skewness0.129
Kurtosis Kurtosis kurtosis-0.412
Angular range angular_range— – 0.3750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5219000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)