4xnv

The human P2Y1 receptor in complex with BPTU

Method: X-RAY DIFFRACTION

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

P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1

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	1-[2-(2-tert-butylphenoxy)pyridin-3-yl]-3-[4-(trifluoromethoxy)phenyl]urea × 1 CHOLESTEROL × 1 CHOLESTEROL HEMISUCCINATE × 3 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 8 PENTAETHYLENE GLYCOL × 1 ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUBR_CLOPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 247–300； UniProt 1–54

P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1

Homo sapiens

UniProt P47900

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	1-[2-(2-tert-butylphenoxy)pyridin-3-yl]-3-[4-(trifluoromethoxy)phenyl]urea × 1 CHOLESTEROL × 1 CHOLESTEROL HEMISUCCINATE × 3 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 8 PENTAETHYLENE GLYCOL × 1 ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P2RY1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–246； UniProt 2–247 Author chain A； PDBConstruct 301–421； UniProt 253–373

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	4xnv
Deposition date deposition_date	2015-01-16
Structure title title	The human P2Y1 receptor in complex with BPTU
Keywords keywords	;human P2Y1 receptor, G protein coupled receptor, platelet activation, membrane protein, inhibitor complex, TRANSPORT PROTEIN-INHIBITOR complex, PSI-Biology, Structural Genomics, GPCR Network, GPCR ;; TRANSPORT PROTEIN/INHIBITOR
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.

4xnv__assembly_1__model_1

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

Download this curve (.dat)

4xnv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4xnv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.31 Å
Rg (electron density)	24.78 Å
Total Rg	25.71 Å
Atom count	3084
Residues	340
Excluded volume	57970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4xnv__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 (8)

Entity 1 Entity 1 polymer

Description description	P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1
Molecular weight formula_weight	47468.3 kDa
Mutation mutation	D320N
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	3114

TEVLWPAVPNGTDAAFLAGPGSSWGNSTVASTAAVSSSFKCALTKTGFQFYYLPAVYILVFIIGFLGNSVAIWMFVFHMKPWSGISVYMFNLALADFLYVLTLPALIFYYFNKTDWIFGDAMCKLQRFIFHVNLYGSILFLTCISAHRYSGVVYPLKSLGRLKKKNAICISVLVWLIVVVAISPILFYSGTGVRKNKTITCYDTTSDEYLRSYFIYSMCTTVAMFCVPLVLILGCYGLIVRALIYKMKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEEPLRRKSIYLVIIVLTVFAVSYIPFHVMKTMNLRARLDFQTPAMCAFNDRVYATYQVTRGLASLNSCVNPILYFLAGDTFRRRLSRATRKASRRSEANLQSKSEDMTLNILPEFKQNGDTSL

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	1-[2-(2-tert-butylphenoxy)pyridin-3-yl]-3-[4-(trifluoromethoxy)phenyl]urea
Molecular weight formula_weight	445.4 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	1

Entity 4 Entity 4 non-polymer

Description description	CHOLESTEROL HEMISUCCINATE
Molecular weight formula_weight	486.7 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 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	8

Entity 6 Entity 6 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	30

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Unit-cell length a length_a	66.270 Å
Unit-cell length b length_b	66.270 Å
Unit-cell length c length_c	239.070 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	41.400 Å
R factor r_factor	0.2078
R_work r_work	0.2066
R_free r_free	0.2303

The human P2Y1 receptor in complex with BPTU

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

P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1

State in the Current Structure

Other States of the Same Protein in the Database

P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1

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

4xnv__assembly_1__model_1

4xnv__assembly_1__model_1 | I(q)

4xnv__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

The human P2Y1 receptor in complex with BPTU

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

P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1

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 1, Rubredoxin, P2Y purinoceptor 1

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

4xnv__assembly_1__model_1

4xnv__assembly_1__model_1 | I(q)

4xnv__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)