6ye9

Small-molecule inhibitor of 14-3-3 protein-protein interactions

Method: X-RAY DIFFRACTION Dmax: 68.6 Å Quality: GOOD

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

14-3-3 protein sigma

Homo sapiens

UniProt P31947

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–231 Not recorded MG MAGNESIUM ION × 6 OO8 [2-[2-oxidanylidene-2-[(phenylmethyl)amino]ethoxy]phenyl]phosphonic acid × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277 K;0.095 M HEPES Na (pH 7.1), 27% (v/v) PEG 400, 0.19 M CaCL2, 5% (v/v) Glycerol Resolution 1.80 Å R-free 0.219

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.

523 other PDB entries and 543 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1433S_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–236; UniProt 1–231

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 6ye9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ye9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ye9
Deposition date deposition_date2020-03-24
Structure title titleSmall-molecule inhibitor of 14-3-3 protein-protein interactions
Keywords keywords14-3-3, Inhibitor, Protein-protein interaction, small molecule, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.47
Radius of gyration Rg (electron density) rg_electron19.32
Forward intensity I(0) i013429100.00
Molecular weight molecular_weight26772.0 kDa
Excluded volume excluded_volume33224 ų
Envelope volume envelope_volume40013 ų
Hydration-shell volume shell_volume17813 ų
Envelope diameter envelope_diameter70.1
Shell Rg shell_rg25.10
Envelope Rg envelope_rg19.70
Shape Rg shape_rg19.31
Total Rg total_rg20.19
Total atoms total_atoms3713
Residues n_residues236
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 dmax68.6
Rg (real space) rg_real20.44
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real1.3430e+07
I(0) uncertainty (real space) i0_real_error1.8970e+05
Rg (reciprocal space) rg_reciprocal20.45
I(0) (reciprocal space) i0_reciprocal13430000.0000
Solution quality estimate total_estimate0.8845
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.5
Skewness Skewness skewness0.299
Kurtosis Kurtosis kurtosis-0.271
Angular range angular_range— – 0.3900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2405000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.941

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6ye9a1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.7 — 14-3-3 protein
Family Family familya.118.7.1 — 14-3-3 protein
Domain ID domain_idd6ye9a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id6ye9A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily20 — 14-3-3 domain

8. Citations (1)

9. Files and Curves (10)