5ewz

Small-molecule stabilization of the 14-3-3/Gab2 PPI interface

Method: X-RAY DIFFRACTION Dmax: 86.2 Å Quality: EXCELLENT

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

14-3-3 protein zeta/delta

Homo sapiens

UniProt P63104

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 1–230 Chain B; UniProt 1–230 Not recorded GRB2-associated-binding protein 2 × 1 (Q9UQC2) GRB2-associated-binding protein 2 × 1 (Q9UQC2) BEZ BENZOIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277.15 K;1.2 M sodium hydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulfate, 0.1 M CAPS Resolution 2.34 Å R-free 0.244

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.

73 other PDB entries and 88 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1433Z_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–230; UniProt 1–230 Author chain B; PDBConstruct 1–230; UniProt 1–230

GRB2-associated-binding protein 2

OrganismNot specified

UniProt Q9UQC2

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 C; UniProt 387–395 Chain D; UniProt 207–212 Non-standard monomer:Yes (specific site not provided by mmCIF) 14-3-3 protein zeta/delta × 2 (P63104) BEZ BENZOIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277.15 K;1.2 M sodium hydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulfate, 0.1 M CAPS Resolution 2.34 Å R-free 0.244

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 GAB2_HUMAN
Isoform
PDB entities 2, 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 387–395 Author chain D; PDBConstruct 1–6; UniProt 207–212

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 5ewz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ewz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ewz
Deposition date deposition_date2015-11-23
Structure title titleSmall-molecule stabilization of the 14-3-3/Gab2 PPI interface
Keywords keywords14-3-3, GAB2, Protein, Diphosphorylation, signaling protein; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.83
Radius of gyration Rg (electron density) rg_electron27.08
Forward intensity I(0) i047859600.00
Molecular weight molecular_weight52783.0 kDa
Excluded volume excluded_volume65690 ų
Envelope volume envelope_volume87816 ų
Hydration-shell volume shell_volume27198 ų
Envelope diameter envelope_diameter91.1
Shell Rg shell_rg34.37
Envelope Rg envelope_rg26.55
Shape Rg shape_rg27.10
Total Rg total_rg27.80
Total atoms total_atoms3703
Residues n_residues469
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 dmax86.2
Rg (real space) rg_real27.79
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real4.7860e+07
I(0) uncertainty (real space) i0_real_error5.9340e+05
Rg (reciprocal space) rg_reciprocal27.81
I(0) (reciprocal space) i0_reciprocal47860000.0000
Solution quality estimate total_estimate0.9145
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.7
Skewness Skewness skewness0.208
Kurtosis Kurtosis kurtosis-0.682
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9122000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.981

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5ewzA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily20 — 14-3-3 domain
Domain ID domain_id5ewzB00
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)