SAXSdb — 9efp

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

SEC14 cytosolic factor

Saccharomyces cerevisiae

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 1–304	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–304	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

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 9EFP	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 construct Different mutation/modification 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 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）	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 mutation/modification 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 mutation/modification 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
7ZGA Structure of yeast Sec14p with ergoline Deposited 2022-04-03	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 3–298（296 aa）	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
7ZGB Structure of yeast Sec14p with NPPM112 Deposited 2022-04-03	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 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 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）	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 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）	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
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 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 9 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 1–304； UniProt 1–304 Author chain B； PDBConstruct 1–304； UniProt 1–304

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	9efp
Deposition date deposition_date	2024-11-20
最后修订 last_revision	2025-11-05
Structure title title	Crystal Structure of Saccharomyces cerevisiae Sec14p in complex with phosphatidylcholine
Keywords keywords	Sec14 PITP Sec14p, 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	28.46 Å
Radius of gyration Rg (electron density) rg_electron	28.00 Å
Forward intensity I(0) i0	70522500.00
Molecular weight molecular_weight	68427.0 kDa
Excluded volume excluded_volume	86723 Å³
Envelope volume envelope_volume	105290 Å³
Hydration-shell volume shell_volume	31559 Å³
Envelope diameter envelope_diameter	92.3 Å
Shell Rg shell_rg	35.06 Å
Envelope Rg envelope_rg	27.86 Å
Shape Rg shape_rg	28.01 Å
Total Rg total_rg	28.72 Å
Total atoms total_atoms	4822
Residues n_residues	577
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	91.0 Å
Rg (real space) rg_real	28.50 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	7.0520e+07
I(0) uncertainty (real space) i0_real_error	1.0770e+06
Rg (reciprocal space) rg_reciprocal	28.49 Å
I(0) (reciprocal space) i0_reciprocal	70520000.0000
Solution quality estimate total_estimate	0.8945
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.2 Å
Skewness Skewness skewness	0.349
Kurtosis Kurtosis kurtosis	-0.505
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18750000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.909

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	SEC14 cytosolic factor
Molecular weight formula_weight	35018.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5126

MVTQQEKEFLESYPQNCPPDALPGTPGNLDSAQEKALAELRKLLEDAGFIERLDDSTLLRFLRARKFDVQLAKEMFENCEKWRKDYGTDTILQDFHYDEKPLIAKFYPQYYHKTDKDGRPVYFEELGAVNLHEMNKVTSEERMLKNLVWEYESVVQYRLPACSRAAGHLVETSCTIMDLKGISISSAYSVMSYVREASYISQNYYPERMGKFYIINAPFGFSTAFRLFKPFLDPVTVSKIFILGSSYQKELLKQIPAENLPVKFGGKSEVDESKGGLYLSDIGPWRDPKYIGPEGEAPEAFSMK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Molecular weight formula_weight	760.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	293

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8. Citations (1)

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Unit-cell length a length_a	74.400 Å
Unit-cell length b length_b	74.400 Å
Unit-cell length c length_c	195.860 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	12

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

Resolution resolution	1.830 Å
Low-resolution limit resolution_low	45.860 Å
R factor r_factor	0.1859
R_work r_work	0.1721
R_free r_free	0.2084

fit	/app/data/saxs_computation/ef/9efp/9efp.fit
pddf	/app/data/pr_computation/ef/9efp/9efp.pr.out
profile	/app/data/saxs_computation/ef/9efp/9efp.dat

Crystal Structure of Saccharomyces cerevisiae Sec14p in complex with phosphatidylcholine

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