SAXSdb — 7zga

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

SEC14 cytosolic factor

Saccharomyces cerevisiae S288C

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 3–298	Not recorded	IUF ~{O}9-methyl ~{O}4-[2,2,2-tris(chloranyl)ethyl] (5~{a}~{S},6~{a}~{S},9~{R},10~{a}~{S})-7-methyl-3-nitro-5,5~{a},6,6~{a},8,9,10,10~{a}-octahydroindolo[4,3-fg]quinoline-4,9-dicarboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；294 K；129,5 mM sodium acetate, 64,8 mM TRIS, 4,6 % (w/v) PEG 4000, and 11.9 % (v/v) glycerol adjusted to pH 7.0	Resolution 2.30 Å R-free 0.228

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 7ZGA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AUA PHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P FROM SACCHAROMYCES CEREVISIAE Deposited 1997-08-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–298（296 aa）	Not recorded	BOG octyl beta-D-glucopyranoside × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；3% PEG 3350, 1% N-OCTYL B-D-GLUCOPYRANOSIDE, 10 MM HEPES, 150MM KCL, PH 7.2	Resolution 2.50 Å R-free 0.273
6F0E Structure of yeast Sec14p with a picolinamide compound Deposited 2017-11-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–304（304 aa）	Not recorded	C8K ~{N}-(1,3-benzodioxol-5-ylmethyl)-5-bromanyl-3-fluoranyl-pyridine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；129.5 mM sodium acetate, 64.8 mM TRIS, 10 % (w/v) PEG 4000, 20 % (v/v) glycerol, pH 7.0	Resolution 2.60 Å R-free 0.226
7ZG9 Structure of yeast Sec14p with himbacine Deposited 2022-04-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–301（299 aa）	Not recorded	KO0 Himbacine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；294 K；129,5 mM sodium acetate, 64,8 mM TRIS, 4,6 % (w/v) PEG 4000, and 11.9 % (v/v) glycerol, pH 7.0	Resolution 1.76 Å R-free 0.222
7ZG9 Structure of yeast Sec14p with himbacine Deposited 2022-04-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 3–301（299 aa）	Not recorded	KO0 Himbacine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；294 K；129,5 mM sodium acetate, 64,8 mM TRIS, 4,6 % (w/v) PEG 4000, and 11.9 % (v/v) glycerol, pH 7.0	Resolution 1.76 Å R-free 0.222
7ZGB Structure of yeast Sec14p with NPPM112 Deposited 2022-04-03	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–299（296 aa）	Not recorded	IUJ 4-fluoranyl-~{N}-[(4-pyrrolidin-1-ylphenyl)methyl]benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；294 K；129,5 mM sodium acetate, 64,8 mM TRIS, 4,6 % (w/v) PEG 4000, and 11.9 % (v/v) glycerol adjusted to pH 7.0	Resolution 2.70 Å R-free 0.249
7ZGC Structure of yeast Sec14p with NPPM481 Deposited 2022-04-03	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–304（304 aa）	Not recorded	IUO (4-chloranyl-3-nitro-phenyl)-[4-(2-fluorophenyl)piperazin-1-yl]methanone × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；294 K；129,5 mM sodium acetate, 64,8 mM TRIS, 4,6 % (w/v) PEG 4000, and 11.9 % (v/v) glycerol adjusted to pH 7.0	Resolution 2.24 Å R-free 0.211
7ZGD Structure of yeast Sec14p with NPPM244 Deposited 2022-04-03	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–304（304 aa）	Not recorded	IUC (4-bromanyl-3-nitro-phenyl)-[4-(2-fluorophenyl)piperazin-1-yl]methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；294 K；129,5 mM sodium acetate, 64,8 mM TRIS, 4,6 % (w/v) PEG 4000, and 11.9 % (v/v) glycerol adjusted to pH 7.0	Resolution 2.08 Å R-free 0.232
9EFP Crystal Structure of Saccharomyces cerevisiae Sec14p in complex with phosphatidylcholine Deposited 2024-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–304（304 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289.15 K；0.1 M Bis-Tris, 30-40% v/v PEG 400, pH 5.5-pH 6.5	Resolution 1.83 Å R-free 0.208
9EFP Crystal Structure of Saccharomyces cerevisiae Sec14p in complex with phosphatidylcholine Deposited 2024-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–304（304 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 1 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289.15 K；0.1 M Bis-Tris, 30-40% v/v PEG 400, pH 5.5-pH 6.5	Resolution 1.83 Å R-free 0.208
9YV3 Crystal Structure of a ternary complex of Saccharomyces cerevisiae Sec14 with a small molecule inhibitor and phosphatidylcholine Deposited 2025-10-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–302（298 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 1 IUO (4-chloranyl-3-nitro-phenyl)-[4-(2-fluorophenyl)piperazin-1-yl]methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；0.05 M ammonium sulfate, 0.05 M Bis Tris 30% v/v pentaeritheytolethoxylate (pH 6.5)	Resolution 2.25 Å R-free 0.268

8 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SEC14_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–296； UniProt 3–298

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	7zga
Deposition date deposition_date	2022-04-03
Structure title title	Structure of yeast Sec14p with ergoline
Keywords keywords	Sec14p, ergoline, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
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	20.18 Å
Radius of gyration Rg (electron density) rg_electron	19.30 Å
Forward intensity I(0) i0	19831200.00
Molecular weight molecular_weight	34459.0 kDa
Excluded volume excluded_volume	43349 Å³
Envelope volume envelope_volume	50769 Å³
Hydration-shell volume shell_volume	21637 Å³
Envelope diameter envelope_diameter	64.8 Å
Shell Rg shell_rg	25.97 Å
Envelope Rg envelope_rg	19.51 Å
Shape Rg shape_rg	19.29 Å
Total Rg total_rg	20.26 Å
Total atoms total_atoms	2429
Residues n_residues	296
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	63.3 Å
Rg (real space) rg_real	20.06 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.9830e+07
I(0) uncertainty (real space) i0_real_error	2.0720e+05
Rg (reciprocal space) rg_reciprocal	20.08 Å
I(0) (reciprocal space) i0_reciprocal	19830000.0000
Solution quality estimate total_estimate	0.8946
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	0.157
Kurtosis Kurtosis kurtosis	-0.404
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4484000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SEC14 cytosolic factor
Molecular weight formula_weight	34017.6 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	2506

TQQEKEFLESYPQNCPPDALPGTPGNLDSAQEKALAELRKLLEDAGFIERLDDSTLLRFLRARKFDVQLAKEMFENCEKWRKDYGTDTILQDFHYDEKPLIAKFYPQYYHKTDKDGRPVYFEELGAVNLHEMNKVTSEERMLKNLVWEYESVVQYRLPACSRAAGHLVETSCTIMDLKGISISSAYSVMSYVREASYISQNYYPERMGKFYIINAPFGFSTAFRLFKPFLDPVTVSKIFILGSSYQKELLKQIPAENLPVKFGGKSEVDESKGGLYLSDIGPWRDPKYIGPEGEAP

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;~{O}9-methyl ~{O}4-[2,2,2-tris(chloranyl)ethyl] (5~{a}~{S},6~{a}~{S},9~{R},10~{a}~{S})-7-methyl-3-nitro-5,5~{a},6,6~{a},8,9,10,10~{a}-octahydroindolo[4,3-fg]quinoline-4,9-dicarboxylate ;
Molecular weight formula_weight	506.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

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8. Citations (1)

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Unit-cell length a length_a	87.498 Å
Unit-cell length b length_b	87.498 Å
Unit-cell length c length_c	110.068 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.302 Å
Low-resolution limit resolution_low	44.529 Å
R factor r_factor	0.1919
R_work r_work	0.1883
R_free r_free	0.2284

fit	/app/data/saxs_computation/zg/7zga/7zga.fit
pddf	/app/data/pr_computation/zg/7zga/7zga.pr.out
profile	/app/data/saxs_computation/zg/7zga/7zga.dat

Structure of yeast Sec14p with ergoline

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

SEC14 cytosolic factor

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