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9yv3

Crystal Structure of a ternary complex of Saccharomyces cerevisiae Sec14 with a small molecule inhibitor and phosphatidylcholine

Method: X-RAY DIFFRACTION D_max: 62.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yv3
deposition_date	2025-10-23
last_revision	2025-11-05
title	Crystal Structure of a ternary complex of Saccharomyces cerevisiae Sec14 with a small molecule inhibitor and phosphatidylcholine
keywords	Sec14 protein, PITP family, LIPID BINDING PROTEIN, SIGNALING PROTEIN; LIPID BINDING PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	20.19 Å
rg_electron	19.32 Å
i0	20202200.00
molecular_weight	35358.0 kDa
excluded_volume	44743 Å³
envelope_volume	51804 Å³
shell_volume	22005 Å³
envelope_diameter	64.2 Å
shell_rg	26.15 Å
envelope_rg	19.51 Å
shape_rg	19.30 Å
total_rg	20.35 Å
total_atoms	2493
n_residues	297
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	62.0 Å
rg_real	20.06 Å
rg_real_error	0.26 Å
i0_real	2.0200e+07
i0_real_error	2.1360e+05
rg_reciprocal	20.09 Å
i0_reciprocal	20200000.0000
total_estimate	0.9010
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.7 Å
skewness	0.147
kurtosis	-0.430
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	4835000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.978

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	SEC14 cytosolic factor
formula_weight	34298.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2700

QEKEFLESYPQNCPPDALPGTPGNLDSAQEKALAELRKLLEDAGFIERLDDSTLLRFLRARKFDVQLAKEMFENCEKWRKDYGTDTILQDFHYDEKPLIAKFYPQYYHKTDKDGRPVYFEELGAVNLHEMNKVTSEERMLKNLVWEYESVVQYRLPACSRAAGHLVETSCTIMDLKGISISSAYSVMSYVREASYISQNYYPERMGKFYIINAPFGFSTAFRLFKPFLDPVTVSKIFILGSSYQKELLKQIPAENLPVKFGGKSEVDESKGGLYLSDIGPWRDPKYIGPEGEAPEAFS

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Escherichia coli

Entity 2 non-polymer

description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
formula_weight	760.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	(4-chloranyl-3-nitro-phenyl)-[4-(2-fluorophenyl)piperazin-1-yl]methanone
formula_weight	363.8 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	193

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6. Citations (1)

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length_a	89.240 Å
length_b	89.240 Å
length_c	100.380 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	2.250 Å
resolution_low	30.710 Å
r_factor	0.2194
r_work	0.2169
r_free	0.2680

fit	/app/data/saxs_computation/yv/9yv3/9yv3.fit
pddf	/app/data/pr_computation/yv/9yv3/9yv3.pr.out
profile	/app/data/saxs_computation/yv/9yv3/9yv3.dat

Crystal Structure of a ternary complex of Saccharomyces cerevisiae Sec14 with a small molecule inhibitor and phosphatidylcholine

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction