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9w0h

S1P3 in complex with cpd-32 and spm242

Method: X-RAY DIFFRACTION D_max: 104.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w0h
deposition_date	2025-07-24
last_revision	2026-06-03
title	S1P3 in complex with cpd-32 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	30.67 Å
rg_electron	30.71 Å
i0	83849700.00
molecular_weight	49735.0 kDa
excluded_volume	48789 Å³
envelope_volume	82652 Å³
shell_volume	24970 Å³
envelope_diameter	105.7 Å
shell_rg	34.08 Å
envelope_rg	30.60 Å
shape_rg	30.69 Å
total_rg	30.98 Å
total_atoms	3765
n_residues	478
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	104.0 Å
rg_real	31.07 Å
rg_real_error	0.87 Å
i0_real	8.3850e+07
i0_real_error	1.4530e+06
rg_reciprocal	30.90 Å
i0_reciprocal	83840000.0000
total_estimate	0.7700
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	24.0 Å
skewness	0.532
kurtosis	-0.553
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0001
highest_alpha	17680000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.598; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.427; Smooth: 0.785

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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	57235.9 kDa
ec_number	3.2.1.8
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3765

PVRGNETLREHYQYVGKLAGRLKEASEGSTLTTVLFLVICSFIVLENLMVLIAIWKNNKFHNRMYFFIGNLALSDLLAGIAYKVNILMSGKKTFSLSPTVWFLREGSMFVALGASTCSLLAIAIERYLTMIKMRPYDANKRHRVFLLIGMCWLIAFTLGALPILGWNCLHNLPDCSTILPLYSKKYIAFCISIFTAILVTIVILYARIYFLVKSASTDYWQNWTFGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDDTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVWNHNNSERSMALLRTVVIVVSVFIACWSPLFILFLIDVACRVQACPILFKAQWFIVLAVLNSAMNPVIYTLASKEMRRAFFRLVCNCLVRGRGARASPIQPALDPSRSKSSSSN

Source

organism	Homo sapiens
common_name	Human
ncbi_taxonomy_id	9606
host_organism	Puma concolor

Entity 2 non-polymer

description	5-bromanyl-~{N}-[(1~{R})-1-[(4-chlorophenyl)amino]-2,2,3,3,3-pentakis(fluoranyl)propyl]pyridine-2-carboxamide
formula_weight	458.6 kDa
src_method	syn
entity_count	1

Entity 3 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

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6. Citations (1)

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length_a	71.911 Å
length_b	301.701 Å
length_c	70.055 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	3.000 Å
resolution_low	38.500 Å
r_factor	0.2436
r_work	0.2424
r_free	0.2678

fit	/app/data/saxs_computation/w0/9w0h/9w0h.fit
pddf	/app/data/pr_computation/w0/9w0h/9w0h.pr.out
profile	/app/data/saxs_computation/w0/9w0h/9w0h.dat

S1P3 in complex with cpd-32 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