SAXSdb — 4ntj

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

P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	ethyl 6-{4-[(benzylsulfonyl)carbamoyl]piperidin-1-yl}-5-cyano-2-methylpyridine-3-carboxylate × 1 CHOLESTEROL × 2 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C562_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 233–338； UniProt 23–128

P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12

Homo sapiens

UniProt Q9H244

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	ethyl 6-{4-[(benzylsulfonyl)carbamoyl]piperidin-1-yl}-5-cyano-2-methylpyridine-3-carboxylate × 1 CHOLESTEROL × 2 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P2Y12_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–232； UniProt 2–223 Author chain A； PDBConstruct 339–457； UniProt 224–342

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	4ntj
Deposition date deposition_date	2013-12-02
Structure title title	Structure of the human P2Y12 receptor in complex with an antithrombotic drug
Keywords keywords	;human P2Y12 receptor, GPCR network, membrane protein, lipidic cubic phase, antithrombotic drug, GPCR, PSI-Biology, Structural Genomics, Signaling Protein, membrane ;; 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.

4ntj__assembly_1__model_1

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

Download this curve (.dat)

4ntj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ntj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.28 Å
Rg (electron density)	30.47 Å
Total Rg	30.96 Å
Atom count	3013
Residues	369
Excluded volume	55320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ntj__assembly_1__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12
Molecular weight formula_weight	53248.9 kDa
Mutation mutation	D294N, M1007W, H1102I, R1106L
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	3025

DYKDDDDGAPQAVDNLTSAPGNTSLCTRDYKITQVLFPLLYTVLFFVGLITNGLAMRIFFQIRSKSNFIIFLKNTVISDLLMILTFPFKILSDAKLGTGPLRTFVCQVTSVIFYFTMYISISFLGLITIDRYQKTTRPFKTSNPKNLLGAKILSVVIWAFMFLLSLPNMILTNRQPRDKNVKKCSFLKSEFGLVWHEIVNYICQVIFWINFLIVIVCYTLITKELYRSYVRTADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLRGVGKVPRKKVNVKVFIIIAVFFICFVPFHFARIPYTLSQTRDVFDCTAENTLFYVKESTLWLTSLNACLNPFIYFFLCKSFRNSLISMLKCPNSATSLSQDNRKKEQDGGDPNEETPMGRPLEVLFQ

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	ethyl 6-{4-[(benzylsulfonyl)carbamoyl]piperidin-1-yl}-5-cyano-2-methylpyridine-3-carboxylate
Molecular weight formula_weight	470.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Molecular weight formula_weight	356.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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Unit-cell length a length_a	98.650 Å
Unit-cell length b length_b	156.430 Å
Unit-cell length c length_c	47.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.620 Å
Low-resolution limit resolution_low	26.440 Å
R factor r_factor	0.2211
R_work r_work	0.2196
R_free r_free	0.2464

Structure of the human P2Y12 receptor in complex with an antithrombotic drug

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

P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12

State in the Current Structure

Other States of the Same Protein in the Database

P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12

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

4ntj__assembly_1__model_1

4ntj__assembly_1__model_1 | I(q)

4ntj__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Structure of the human P2Y12 receptor in complex with an antithrombotic drug

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

P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12

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

4ntj__assembly_1__model_1

4ntj__assembly_1__model_1 | I(q)

4ntj__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)