SAXSdb — 9w0l

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

Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	[(2~{R})-2-azanyl-4-[2-chloranyl-4-(3-hydroxyphenyl)sulfanyl-phenyl]-2-(hydroxymethyl)butyl] dihydrogen phosphate × 2 ~{N}-[(~{R})-(5-bromanylpyridin-2-yl)-(3,4-dichlorophenyl)methyl]-4-cyano-3-fluoranyl-benzamide × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XYNA_NIACI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 210–394； UniProt 29–213

Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase

Homo sapiens

UniProt Q99500

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	[(2~{R})-2-azanyl-4-[2-chloranyl-4-(3-hydroxyphenyl)sulfanyl-phenyl]-2-(hydroxymethyl)butyl] dihydrogen phosphate × 2 ~{N}-[(~{R})-(5-bromanylpyridin-2-yl)-(3,4-dichlorophenyl)methyl]-4-cyano-3-fluoranyl-benzamide × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S1PR3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–209； UniProt 16–224 Author chain A； PDBConstruct 395–484； UniProt 231–320

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	9w0l
Deposition date deposition_date	2025-07-24
Last revision last_revision	2026-06-03
Structure title title	S1P3 in complex with CYM52581 and spm242
Keywords keywords	S1P3, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9w0l__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9w0l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9w0l__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	35.70 Å
Rg (electron density)	34.79 Å
Total Rg	35.10 Å
Atom count	7496
Residues	954
Excluded volume	134480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9w0l__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase
Molecular weight formula_weight	54355.7 kDa
EC 编号 ec_number	3.2.1.8
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3748

ETLREHYQYVGKLAGRLKEASEGSTLTTVLFLVICSFIVLENLMVLIAIWKNNKFHNRMYFFIGNLALSDLLAGIAYKVNILMSGKKTFSLSPTVWFLREGSMFVALGASTCSLLAIAIERYLTMIKMRPYDANKRHRVFLLIGMCWLIAFTLGALPILGWNCLHNLPDCSTILPLYSKKYIAFCISIFTAILVTIVILYARIYFLVKSASTDYWQNWTFGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDDTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVWNHNNSERSMALLRTVVIVVSVFIACWSPLFILFLIDVACRVQACPILFKAQWFIVLAVLNSAMNPVIYTLASKEMRRAFFRLVCNCLVRG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Puma concolor

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

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

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Unit-cell length a length_a	73.570 Å
Unit-cell length b length_b	299.580 Å
Unit-cell length c length_c	67.460 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	29.660 Å
R factor r_factor	0.2338
R_work r_work	0.2314
R_free r_free	0.2810

S1P3 in complex with CYM52581 and spm242

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

Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase

State in the Current Structure

Other States of the Same Protein in the Database

Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9w0l__assembly_1__model_1

9w0l__assembly_1__model_1 | I(q)

9w0l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)

S1P3 in complex with CYM52581 and spm242

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

Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9w0l__assembly_1__model_1

9w0l__assembly_1__model_1 | I(q)

9w0l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)