7b9d

Notum Fragment 290

Method: X-RAY DIFFRACTION Dmax: 65.6 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 × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 T3N 2-(4-acetamidophenoxy)ethanoic acid × 1 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 1.93 Å R-free 0.264

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 7b9d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7b9d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7b9d
Deposition date deposition_date2020-12-14
Structure title titleNotum Fragment 290
Keywords keywordsNotum Inhibitor, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.00
Radius of gyration Rg (electron density) rg_electron19.52
Forward intensity I(0) i026300200.00
Molecular weight molecular_weight38057.0 kDa
Excluded volume excluded_volume47022 ų
Envelope volume envelope_volume54961 ų
Hydration-shell volume shell_volume22826 ų
Envelope diameter envelope_diameter65.5
Shell Rg shell_rg26.74
Envelope Rg envelope_rg19.86
Shape Rg shape_rg19.48
Total Rg total_rg20.52
Total atoms total_atoms2677
Residues n_residues336
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 dmax65.6
Rg (real space) rg_real20.84
Rg uncertainty (real space) rg_real_error0.31
I(0) (real space) i0_real2.6300e+07
I(0) uncertainty (real space) i0_real_error3.3060e+05
Rg (reciprocal space) rg_reciprocal20.87
I(0) (reciprocal space) i0_reciprocal26300000.0000
Solution quality estimate total_estimate0.8963
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.6
Skewness Skewness skewness0.088
Kurtosis Kurtosis kurtosis-0.466
Angular range angular_range— – 0.3800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4707000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.989

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)