5okf

CH1 chimera of human 14-3-3 sigma with the HSPB6 phosphopeptide in a conformation with self-bound phosphopeptides

Method: X-RAY DIFFRACTION Dmax: 101.4 Å Quality: GOOD

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

14-3-3 protein sigma,Heat shock protein beta-6

Homo sapiens

UniProt O14558

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 12–19 Chain B; UniProt 12–19 Fragment:;Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19 ; Non-standard monomer:Yes (specific site not provided by mmCIF) CD CADMIUM ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1 M HEPES buffer (pH 7.5), 1 M Naacetate, and 50 mM cadmium sulfate Resolution 3.20 Å R-free 0.279
2 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 12–19 Chain D; UniProt 12–19 Fragment:;Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19 ; Non-standard monomer:Yes (specific site not provided by mmCIF) CD CADMIUM ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1 M HEPES buffer (pH 7.5), 1 M Naacetate, and 50 mM cadmium sulfate Resolution 3.20 Å R-free 0.279

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.

7 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HSPB6_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 239–246; UniProt 12–19 Author chain B; PDBConstruct 239–246; UniProt 12–19 Author chain C; PDBConstruct 239–246; UniProt 12–19 Author chain D; PDBConstruct 239–246; UniProt 12–19

14-3-3 protein sigma,Heat shock protein beta-6

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 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–231 Chain B; UniProt 1–231 Fragment:;Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19 ; Non-standard monomer:Yes (specific site not provided by mmCIF) CD CADMIUM ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1 M HEPES buffer (pH 7.5), 1 M Naacetate, and 50 mM cadmium sulfate Resolution 3.20 Å R-free 0.279
2 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–231 Chain D; UniProt 1–231 Fragment:;Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19 ; Non-standard monomer:Yes (specific site not provided by mmCIF) CD CADMIUM ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1 M HEPES buffer (pH 7.5), 1 M Naacetate, and 50 mM cadmium sulfate Resolution 3.20 Å R-free 0.279

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 542 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 4–234; UniProt 1–231 Author chain B; PDBConstruct 4–234; UniProt 1–231 Author chain C; PDBConstruct 4–234; UniProt 1–231 Author chain D; PDBConstruct 4–234; 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 5okf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5okf
Deposition date deposition_date2017-07-25
Structure title titleCH1 chimera of human 14-3-3 sigma with the HSPB6 phosphopeptide in a conformation with self-bound phosphopeptides
Keywords keywords14-3-3 proteins, Protein chimera, phosphopeptide-binding, 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_guinier31.90
Radius of gyration Rg (electron density) rg_electron31.22
Forward intensity I(0) i0193453000.00
Molecular weight molecular_weight105880.0 kDa
Excluded volume excluded_volume130000 ų
Envelope volume envelope_volume168820 ų
Hydration-shell volume shell_volume45033 ų
Envelope diameter envelope_diameter107.2
Shell Rg shell_rg38.59
Envelope Rg envelope_rg30.86
Shape Rg shape_rg31.24
Total Rg total_rg31.74
Total atoms total_atoms14348
Residues n_residues912
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 dmax101.4
Rg (real space) rg_real31.74
Rg uncertainty (real space) rg_real_error0.64
I(0) (real space) i0_real1.9350e+08
I(0) uncertainty (real space) i0_real_error2.8620e+06
Rg (reciprocal space) rg_reciprocal31.81
I(0) (reciprocal space) i0_reciprocal193500000.0000
Solution quality estimate total_estimate0.8905
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.6
Skewness Skewness skewness0.193
Kurtosis Kurtosis kurtosis-0.335
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26650000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.917

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5okfA00
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_id5okfB00
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_id5okfC00
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_id5okfD00
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)