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6f0e

Structure of yeast Sec14p with a picolinamide compound

Method: X-RAY DIFFRACTION Dmax: 61.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SEC14 cytosolic factor

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P24280

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 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

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 6F0E 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 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
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
7ZGA Structure of yeast Sec14p with ergoline 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 3–298（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 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 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 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
9EFP Crystal Structure of Saccharomyces cerevisiae Sec14p in complex with phosphatidylcholine Deposited 2024-11-20 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）
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 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 9–312； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 6f0e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6f0e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6f0e
Deposition date deposition_date2017-11-20
Structure title titleStructure of yeast Sec14p with a picolinamide compound
Keywords keywords;Sec14p, lipid transfer protein, chemogenomics, target identification, functional variomics, co-crystal, antifungal, benzamide, picolinamide, lipid binding protein ;; LIPID BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.05 Å
Radius of gyration Rg (electron density) rg_electron19.13 Å
Forward intensity I(0) i019603500.00
Molecular weight molecular_weight33959.0 kDa
Excluded volume excluded_volume42537 ų
Envelope volume envelope_volume49717 ų
Hydration-shell volume shell_volume21373 ų
Envelope diameter envelope_diameter63.2 Å
Shell Rg shell_rg25.86 Å
Envelope Rg envelope_rg19.30 Å
Shape Rg shape_rg19.14 Å
Total Rg total_rg20.04 Å
Total atoms total_atoms2396
Residues n_residues300
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax61.2 Å
Rg (real space) rg_real19.93 Å
Rg uncertainty (real space) rg_real_error0.29 Å
I(0) (real space) i0_real1.9600e+07
I(0) uncertainty (real space) i0_real_error2.2190e+05
Rg (reciprocal space) rg_reciprocal19.96 Å
I(0) (reciprocal space) i0_reciprocal19600000.0000
Solution quality estimate total_estimate0.9030
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.2 Å
Skewness Skewness skewness0.146
Kurtosis Kurtosis kurtosis-0.429
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4475000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6f0ea1
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.3 — CRAL/TRIO N-terminal domain
Family Family familya.5.3.0 — automated matches
Domain ID domain_idd6f0ea2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.13 — SpoIIaa-like
Superfamily Superfamily superfamilyc.13.1 — CRAL/TRIO domain
Family Family familyc.13.1.1 — CRAL/TRIO domain

CATH v4.4 (2 domains)

Domain ID domain_id6f0eA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily20 — N-terminal domain of phosphatidylinositol transfer protein sec14p
Domain ID domain_id6f0eA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology525 — Phosphatidylinositol Transfer Protein Sec14p
Homologous superfamily homologous superfamily10 — CRAL-TRIO lipid binding domain
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8. Citations (1)

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9. Files and Curves (10)