SAXSdb — 3ual

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

14-3-3 protein epsilon

Homo sapiens

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 1–232	Fragment：UNP residues 1-232	Myeloid leukemia factor 1 × 2 （P58340） TBU TERTIARY-BUTYL ALCOHOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M Na-Citrate, 35% tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.222
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–232	Fragment：UNP residues 1-232	Myeloid leukemia factor 1 × 1 （P58340） TBU TERTIARY-BUTYL ALCOHOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M Na-Citrate, 35% tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.222

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.

Other PDB	Difference from Current Entry 3UAL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BR9 14-3-3 Protein Epsilon (Human) Complexed to Peptide Deposited 2005-05-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–233（233 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；40% MPD, 5% PEG10000, 0.1M CACODYLATE PH6.5. PROTEIN IN 150MM NACL, 50MM TRIS PH8, pH 8.00	Resolution 1.75 Å R-free 0.239
3UBW Complex of 14-3-3 isoform epsilon, a Mlf1 phosphopeptide and a small fragment hit from a FBDD screen Deposited 2011-10-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–234（234 aa） Fragment：delta C, UNP residues 1-234	Non-standard monomer：Yes (specific site not provided by mmCIF)	TBU TERTIARY-BUTYL ALCOHOL × 10 6SP (3S)-pyrrolidin-3-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；For crystallization of the 14-3-3 /MLF129-42 peptide complex, protein and peptide were mixed in a 1:1.5 molar ratio in 20 mM Hepes/NaOH pH 7.5, 2 mM MgCl2 and 2 mM 2-ME and set up for crystallization in 0.1 M Na-Citrate pH 5.6 and 35% tert-butanol at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.238
3UBW Complex of 14-3-3 isoform epsilon, a Mlf1 phosphopeptide and a small fragment hit from a FBDD screen Deposited 2011-10-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–234（234 aa） Fragment：delta C, UNP residues 1-234	Non-standard monomer：Yes (specific site not provided by mmCIF)	TBU TERTIARY-BUTYL ALCOHOL × 5 6SP (3S)-pyrrolidin-3-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；For crystallization of the 14-3-3 /MLF129-42 peptide complex, protein and peptide were mixed in a 1:1.5 molar ratio in 20 mM Hepes/NaOH pH 7.5, 2 mM MgCl2 and 2 mM 2-ME and set up for crystallization in 0.1 M Na-Citrate pH 5.6 and 35% tert-butanol at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.238
6EIH The crystal structure of 14-3-3 epsilon in complex with the phosphorylated NELFE peptide Deposited 2017-09-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 3–232（230 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；40% pentaerythritol propoxylate, 0.2M sodium thiocyanate, 0.1M HEPES, pH 7.0	Resolution 2.70 Å R-free 0.241
7C8E Crystal Structure of 14-3-3 epsilon with 9J10 peptide Deposited 2020-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–232（232 aa） Chain B 1–232（232 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289.15 K；28% PEG 400, 0.1M Hepes pH 7.5, 0.2M Calcium chloride	Resolution 3.16 Å R-free 0.271
8DGM 14-3-3 epsilon bound to phosphorylated PEAK1 (pT1165) peptide Deposited 2022-06-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–255（255 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.8 M ammonium sulfate, 0.1 M HEPES pH 7.5, 5% (v/v) MPD	Resolution 3.20 Å R-free 0.266
8DGN 14-3-3 epsilon bound to phosphorylated PEAK2 (pS826) peptide Deposited 2022-06-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–255（255 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.8 M ammonium sulfate, 0.1 M HEPES pH 7.5, 5% (v/v) MPD	Resolution 3.16 Å R-free 0.295
8DGP 14-3-3 epsilon bound to phosphorylated PEAK3 (pS69) peptide Deposited 2022-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–255（255 aa） Chain B 1–255（255 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.35；293 K；2M ammonium sulfate, 0.1 M sodium bicine pH 9.35, 5% (v/v) 2-methyl-2,4,-pentandiol (MPD)	Resolution 2.70 Å R-free 0.233
8DGP 14-3-3 epsilon bound to phosphorylated PEAK3 (pS69) peptide Deposited 2022-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–255（255 aa） Chain D 1–255（255 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.35；293 K；2M ammonium sulfate, 0.1 M sodium bicine pH 9.35, 5% (v/v) 2-methyl-2,4,-pentandiol (MPD)	Resolution 2.70 Å R-free 0.233
8DP5 Structure of the PEAK3/14-3-3 complex Deposited 2022-07-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–255（255 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；A final concentration of 0.1% of Octyl-beta-Glucoside (C14H28O6) was added to the sample before freezing. cryo-EM vitrification conditions Cryogen ETHANE；blot time = 7s blot force = 4	Resolution 3.10 Å
8Q1S Pathogenic mutations of human phosphorylation sites affect protein-protein interactions Deposited 2023-08-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–255（255 aa） Chain B 1–255（255 aa）	Not recorded	BR BROMIDE ION × 1 EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；19% PEG 3350, 0.35 M NaBr, 0.1 M BisTris-Propane pH 6.5	Resolution 3.23 Å R-free 0.279

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	1433E_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–232； UniProt 1–232

Myeloid leukemia factor 1

OrganismNot specified

UniProt P58340

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 29–42	Fragment：UNP residues 29-42 Non-standard monomer：Yes (specific site not provided by mmCIF)	14-3-3 protein epsilon × 2 （P62258） TBU TERTIARY-BUTYL ALCOHOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M Na-Citrate, 35% tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.222
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain P； UniProt 29–42	Fragment：UNP residues 29-42 Non-standard monomer：Yes (specific site not provided by mmCIF)	14-3-3 protein epsilon × 1 （P62258） TBU TERTIARY-BUTYL ALCOHOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M Na-Citrate, 35% tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.222

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.

Other PDB	Difference from Current Entry 3UAL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3UBW Complex of 14-3-3 isoform epsilon, a Mlf1 phosphopeptide and a small fragment hit from a FBDD screen Deposited 2011-10-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 29–42（14 aa） Fragment：phospho- 14-3-3 binding motif, UNP residues 29-42	Non-standard monomer：Yes (specific site not provided by mmCIF)	TBU TERTIARY-BUTYL ALCOHOL × 10 6SP (3S)-pyrrolidin-3-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；For crystallization of the 14-3-3 /MLF129-42 peptide complex, protein and peptide were mixed in a 1:1.5 molar ratio in 20 mM Hepes/NaOH pH 7.5, 2 mM MgCl2 and 2 mM 2-ME and set up for crystallization in 0.1 M Na-Citrate pH 5.6 and 35% tert-butanol at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.238
3UBW Complex of 14-3-3 isoform epsilon, a Mlf1 phosphopeptide and a small fragment hit from a FBDD screen Deposited 2011-10-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 29–42（14 aa） Fragment：phospho- 14-3-3 binding motif, UNP residues 29-42	Non-standard monomer：Yes (specific site not provided by mmCIF)	TBU TERTIARY-BUTYL ALCOHOL × 5 6SP (3S)-pyrrolidin-3-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；For crystallization of the 14-3-3 /MLF129-42 peptide complex, protein and peptide were mixed in a 1:1.5 molar ratio in 20 mM Hepes/NaOH pH 7.5, 2 mM MgCl2 and 2 mM 2-ME and set up for crystallization in 0.1 M Na-Citrate pH 5.6 and 35% tert-butanol at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.238

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MLF1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–14； UniProt 29–42

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ual
Deposition date deposition_date	2011-10-21
Structure title title	Crystal Structure of 14-3-3 epsilon with Mlf1 peptide
Keywords keywords	Adapter protein, ALL HELICAL, PHOSPHOPETIDE, SIGNALING PROTEIN-PROTEIN BINDING complex; SIGNALING PROTEIN/PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	19.94 Å
Radius of gyration Rg (electron density) rg_electron	18.84 Å
Forward intensity I(0) i0	13632000.00
Molecular weight molecular_weight	27477.0 kDa
Excluded volume excluded_volume	34397 Å³
Envelope volume envelope_volume	40481 Å³
Hydration-shell volume shell_volume	18278 Å³
Envelope diameter envelope_diameter	68.0 Å
Shell Rg shell_rg	25.04 Å
Envelope Rg envelope_rg	19.31 Å
Shape Rg shape_rg	18.81 Å
Total Rg total_rg	19.90 Å
Total atoms total_atoms	1927
Residues n_residues	237
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	65.0 Å
Rg (real space) rg_real	19.91 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.3630e+07
I(0) uncertainty (real space) i0_real_error	1.8500e+05
Rg (reciprocal space) rg_reciprocal	19.91 Å
I(0) (reciprocal space) i0_reciprocal	13630000.0000
Solution quality estimate total_estimate	0.8113
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.321
Kurtosis Kurtosis kurtosis	-0.218
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2605000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	14-3-3 protein epsilon
Molecular weight formula_weight	26617.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2175

MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Myeloid leukemia factor 1
Molecular weight formula_weight	1749.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MIRSFSEPFGRDLL

Entity 3 Entity 3 non-polymer

Description description	TERTIARY-BUTYL ALCOHOL
Molecular weight formula_weight	74.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	159

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3uala_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.7 — 14-3-3 protein
Family Family family	a.118.7.1 — 14-3-3 protein

CATH v4.4 (1 domains)

Domain ID domain_id	3ualA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily	20 — 14-3-3 domain

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8. Citations (1)

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Unit-cell length a length_a	77.980 Å
Unit-cell length b length_b	81.460 Å
Unit-cell length c length_c	82.840 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	35.270 Å
R factor r_factor	0.1744
R_work r_work	0.1719
R_free r_free	0.2224

fit	/app/data/saxs_computation/ua/3ual/3ual.fit
pddf	/app/data/pr_computation/ua/3ual/3ual.pr.out
profile	/app/data/saxs_computation/ua/3ual/3ual.dat

Crystal Structure of 14-3-3 epsilon with Mlf1 peptide

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

14-3-3 protein epsilon

State in the Current Structure

Other States of the Same Protein in the Database

Myeloid leukemia factor 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)