SAXSdb — 5svk

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

P2X purinoceptor 3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 3 其他Polymer 6	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 6 ADENOSINE-5'-TRIPHOSPHATE × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 1,2-ETHANEDIOL × 3 (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID × 3 water × 3	Consistent with protein count
2	Other combination	Homooligomer	Protein 3 其他Polymer 6	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 6 ADENOSINE-5'-TRIPHOSPHATE × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 1,2-ETHANEDIOL × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P2RX3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–363； UniProt 6–364 Author chain B； PDBConstruct 5–363； UniProt 6–364

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	5svk
Deposition date deposition_date	2016-08-06
Structure title title	Crystal structure of the ATP-gated human P2X3 ion channel in the ATP-bound, open state
Keywords keywords	Membrane protein, Ion Channel, Open State; 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.

5svk__assembly_1__model_1

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

Download this curve (.dat)

5svk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5svk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.79 Å
Rg (electron density)	36.85 Å
Total Rg	37.25 Å
Atom count	8974
Residues	1071
Excluded volume	156970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5svk__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5svk__assembly_2__model_1`	trimeric （3）	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 (7)

Entity 1 Entity 1 polymer

Description description	P2X purinoceptor 3
Molecular weight formula_weight	40745.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5967

GSRADFFTYETPKVIVVKSWTIGIINRVVQLLIISYFVGWVFLHEKAYQVRDTAIESSVVTKVKGSGLYANRVMDVSDYVTPPQGTSVFVIITKMIVTENQMQGFCPESEEKYRCVSDSQCGPERLPGGGILTGRCVNYSSVLRTCEIQGWCPTEVDTVETPIMMEAENFTIFIKNSIRFPLFNFEKGNLLPNLTARDMKTCRFHPDKDPFCPILRVGDVVKFAGQDFAKLARTGGVLGIKIGWVCDLDKAWDQCIPKYSFTRLDSVSEKSSVSPGYNFRFAKYYKMENGSEYRTLLKAFGIRFDVLVYGNAGKFNIIPTIISSVAAFTSVGVGTVLCDIILLNFLKGADQYKAKKFEEVNET

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID
Molecular weight formula_weight	190.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	61

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5svkA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	490 — atp-gated p2x4 ion channel fold
Homologous superfamily homologous superfamily	10 — atp-gated p2x4 ion channel domain

Domain ID domain_id	5svkB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	490 — atp-gated p2x4 ion channel fold
Homologous superfamily homologous superfamily	10 — atp-gated p2x4 ion channel domain

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Unit-cell length a length_a	173.150 Å
Unit-cell length b length_b	173.150 Å
Unit-cell length c length_c	173.150 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	24

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.773 Å
Low-resolution limit resolution_low	43.287 Å
R factor r_factor	0.2019
R_work r_work	0.2005
R_free r_free	0.2277

Crystal structure of the ATP-gated human P2X3 ion channel in the ATP-bound, open state

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

P2X purinoceptor 3

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

5svk__assembly_1__model_1

5svk__assembly_1__model_1 | I(q)

5svk__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the ATP-gated human P2X3 ion channel in the ATP-bound, open state

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

P2X purinoceptor 3

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

5svk__assembly_1__model_1

5svk__assembly_1__model_1 | I(q)

5svk__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)