6s39

Fragment AZ-018 binding at the p53pT387/14-3-3 sigma interface

Method: X-RAY DIFFRACTION Dmax: 63.6 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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–248 Not recorded Cellular tumor antigen p53 × 2 (P04637) K5Z 5-(3-azanylpropyl)-4-phenyl-thiophene-2-carboximidamide × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT. Resolution 1.88 Å R-free 0.388

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 6–253; UniProt 1–248

Cellular tumor antigen p53

OrganismNot specified

UniProt P04637

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain P; UniProt 382–393 Non-standard monomer:Yes (specific site not provided by mmCIF) 14-3-3 protein sigma × 2 (P31947) K5Z 5-(3-azanylpropyl)-4-phenyl-thiophene-2-carboximidamide × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT. Resolution 1.88 Å R-free 0.388

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.

291 other PDB entries and 462 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name P53_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain P; PDBConstruct 1–12; UniProt 382–393

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 6s39

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6s39
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6s39
Deposition date deposition_date2019-06-24
Structure title titleFragment AZ-018 binding at the p53pT387/14-3-3 sigma interface
Keywords keywordsprotein protein interaction, fragment soaking, stabilization, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.44
Radius of gyration Rg (electron density) rg_electron18.32
Forward intensity I(0) i013661600.00
Molecular weight molecular_weight27108.0 kDa
Excluded volume excluded_volume33687 ų
Envelope volume envelope_volume39586 ų
Hydration-shell volume shell_volume18234 ų
Envelope diameter envelope_diameter66.1
Shell Rg shell_rg24.55
Envelope Rg envelope_rg18.71
Shape Rg shape_rg18.31
Total Rg total_rg19.27
Total atoms total_atoms1896
Residues n_residues238
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 dmax63.6
Rg (real space) rg_real19.36
Rg uncertainty (real space) rg_real_error0.41
I(0) (real space) i0_real1.3660e+07
I(0) uncertainty (real space) i0_real_error1.7030e+05
Rg (reciprocal space) rg_reciprocal19.37
I(0) (reciprocal space) i0_reciprocal13660000.0000
Solution quality estimate total_estimate0.8088
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.2
Skewness Skewness skewness0.244
Kurtosis Kurtosis kurtosis-0.317
Angular range angular_range— – 0.4100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2930000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.839; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id6s39A01
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)