6rp6

Fragment AZ-019 binding at the TAZpS89/14-3-3 sigma interface

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–231 Not recorded WW domain-containing transcription regulator protein 1 × 2 (Q9GZV5) KDK 4-phenyl-5-(piperidin-4-ylmethyl)thiophene-2-carboximidamide × 2 CA CALCIUM ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.1;277 K;0.095 M Na-HEPES pH 7.1, 27% PEG400, 0.19 M Calcium chloride, 5% Glycerol Resolution 1.89 Å R-free 0.220

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

WW domain-containing transcription regulator protein 1

OrganismNot specified

UniProt Q9GZV5

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 86–98 Non-standard monomer:Yes (specific site not provided by mmCIF) 14-3-3 protein sigma × 2 (P31947) KDK 4-phenyl-5-(piperidin-4-ylmethyl)thiophene-2-carboximidamide × 2 CA CALCIUM ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.1;277 K;0.095 M Na-HEPES pH 7.1, 27% PEG400, 0.19 M Calcium chloride, 5% Glycerol Resolution 1.89 Å R-free 0.220

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WWTR1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain P; PDBConstruct 1–13; UniProt 86–98

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 6rp6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6rp6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6rp6
Deposition date deposition_date2019-05-14
Structure title titleFragment AZ-019 binding at the TAZpS89/14-3-3 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_guinier20.02
Radius of gyration Rg (electron density) rg_electron18.88
Forward intensity I(0) i013843400.00
Molecular weight molecular_weight27271.0 kDa
Excluded volume excluded_volume33894 ų
Envelope volume envelope_volume40096 ų
Hydration-shell volume shell_volume18060 ų
Envelope diameter envelope_diameter69.9
Shell Rg shell_rg24.99
Envelope Rg envelope_rg19.48
Shape Rg shape_rg18.89
Total Rg total_rg19.77
Total atoms total_atoms3749
Residues n_residues245
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_real19.99
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real1.3840e+07
I(0) uncertainty (real space) i0_real_error1.5730e+05
Rg (reciprocal space) rg_reciprocal20.00
I(0) (reciprocal space) i0_reciprocal13840000.0000
Solution quality estimate total_estimate0.8746
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.5
Skewness Skewness skewness0.336
Kurtosis Kurtosis kurtosis-0.207
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2847000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id6rp6A01
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)