6yr7

14-3-3 sigma in complex with hDMX-342+367 peptide

Method: X-RAY DIFFRACTION Dmax: 84.5 Å Quality: EXCELLENT

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 Chain B; UniProt 1–231 Not recorded Protein Mdm4 × 2 (O15151) B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;277 K;Sodium citrate tribasic dihydrate, PEG3350, Bis-Tris propane pH8 Resolution 2.10 Å R-free 0.246

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 Author chain B; PDBConstruct 6–236; UniProt 1–231

Protein Mdm4

OrganismNot specified

UniProt O15151

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 335–374 Chain Q; UniProt 335–374 Non-standard monomer:Yes (specific site not provided by mmCIF) 14-3-3 protein sigma × 2 (P31947) B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;277 K;Sodium citrate tribasic dihydrate, PEG3350, Bis-Tris propane pH8 Resolution 2.10 Å R-free 0.246

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.

36 other PDB entries and 66 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MDM4_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–40; UniProt 335–374 Author chain Q; PDBConstruct 1–40; UniProt 335–374

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 6yr7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6yr7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6yr7
Deposition date deposition_date2020-04-19
Structure title title14-3-3 sigma in complex with hDMX-342+367 peptide
Keywords keywordsbivalent binding mode, 1433, 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_guinier27.52
Radius of gyration Rg (electron density) rg_electron26.60
Forward intensity I(0) i047545600.00
Molecular weight molecular_weight52031.0 kDa
Excluded volume excluded_volume64472 ų
Envelope volume envelope_volume82384 ų
Hydration-shell volume shell_volume26088 ų
Envelope diameter envelope_diameter87.1
Shell Rg shell_rg33.63
Envelope Rg envelope_rg26.10
Shape Rg shape_rg26.60
Total Rg total_rg27.34
Total atoms total_atoms7153
Residues n_residues472
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 dmax84.5
Rg (real space) rg_real27.50
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real4.7550e+07
I(0) uncertainty (real space) i0_real_error6.4180e+05
Rg (reciprocal space) rg_reciprocal27.51
I(0) (reciprocal space) i0_reciprocal47550000.0000
Solution quality estimate total_estimate0.9136
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.1
Skewness Skewness skewness0.220
Kurtosis Kurtosis kurtosis-0.691
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8381000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.958

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6yr7A01
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_id6yr7B01
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)