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9w0l

S1P3 in complex with CYM52581 and spm242

Method: X-RAY DIFFRACTION D_max: 103.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w0l
deposition_date	2025-07-24
last_revision	2026-06-03
title	S1P3 in complex with CYM52581 and spm242
keywords	S1P3, MEMBRANE PROTEIN; MEMBRANE 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	30.63 Å
rg_electron	30.65 Å
i0	82359000.00
molecular_weight	49500.0 kDa
excluded_volume	48647 Å³
envelope_volume	81189 Å³
shell_volume	24518 Å³
envelope_diameter	105.4 Å
shell_rg	34.11 Å
envelope_rg	30.68 Å
shape_rg	30.64 Å
total_rg	30.91 Å
total_atoms	3748
n_residues	477
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	103.8 Å
rg_real	31.04 Å
rg_real_error	0.87 Å
i0_real	8.2360e+07
i0_real_error	1.4250e+06
rg_reciprocal	30.87 Å
i0_reciprocal	82350000.0000
total_estimate	0.7619
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	24.0 Å
skewness	0.529
kurtosis	-0.574
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0001
highest_alpha	15950000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.580; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.395; Smooth: 0.766

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase
formula_weight	54355.7 kDa
ec_number	3.2.1.8
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3748

ETLREHYQYVGKLAGRLKEASEGSTLTTVLFLVICSFIVLENLMVLIAIWKNNKFHNRMYFFIGNLALSDLLAGIAYKVNILMSGKKTFSLSPTVWFLREGSMFVALGASTCSLLAIAIERYLTMIKMRPYDANKRHRVFLLIGMCWLIAFTLGALPILGWNCLHNLPDCSTILPLYSKKYIAFCISIFTAILVTIVILYARIYFLVKSASTDYWQNWTFGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDDTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVWNHNNSERSMALLRTVVIVVSVFIACWSPLFILFLIDVACRVQACPILFKAQWFIVLAVLNSAMNPVIYTLASKEMRRAFFRLVCNCLVRG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Puma concolor

Entity 2 non-polymer

description	[(2~{R})-2-azanyl-4-[2-chloranyl-4-(3-hydroxyphenyl)sulfanyl-phenyl]-2-(hydroxymethyl)butyl] dihydrogen phosphate
formula_weight	433.8 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	~{N}-[(~{R})-(5-bromanylpyridin-2-yl)-(3,4-dichlorophenyl)methyl]-4-cyano-3-fluoranyl-benzamide
formula_weight	479.1 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	73.570 Å
length_b	299.580 Å
length_c	67.460 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	3.600 Å
resolution_low	29.660 Å
r_factor	0.2338
r_work	0.2314
r_free	0.2810

fit	/app/data/saxs_computation/w0/9w0l/9w0l.fit
pddf	/app/data/pr_computation/w0/9w0l/9w0l.pr.out
profile	/app/data/saxs_computation/w0/9w0l/9w0l.dat

S1P3 in complex with CYM52581 and spm242

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