SAXSdb — 5ygv

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

Abscisic acid receptor PYR1

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(2Z,4E)-3-methyl-5-[(1S,4S)-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic acid × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYR1_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 37–227； UniProt 1–191 Author chain B； PDBConstruct 37–227； UniProt 1–191

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	5ygv
Deposition date deposition_date	2017-09-27
Structure title title	Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist
Keywords keywords	Hormone receptor; HORMONE RECEPTOR
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.

5ygv__assembly_1__model_1

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

Download this curve (.dat)

5ygv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ygv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.17 Å
Rg (electron density)	22.84 Å
Total Rg	23.69 Å
Atom count	2801
Residues	340
Excluded volume	49878 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ygv__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	Abscisic acid receptor PYR1
Molecular weight formula_weight	25432.5 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	2819

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFMPSELTPEERSELKNSIAEFHTYQLDPGSCSSLHAQRIHAPPELVWSIVRRFDKPQTYKHFIKSCSVEQNFEMRVGCTRDVIVISGLPANTSTERLDILDDERRVTGFSIIGGEHRLTNYKSVTTVHRFEKENRIWTVVLESYVVDMPEGNSEDDTRMFADTVVKLNLQKLATVAEAMARNSGDGSGSQVT

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	(2Z,4E)-3-methyl-5-[(1S,4S)-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic acid
Molecular weight formula_weight	394.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	18

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ygvA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
Homologous superfamily homologous superfamily	20 — START domain

Domain ID domain_id	5ygvB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
Homologous superfamily homologous superfamily	20 — START domain

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Unit-cell length a length_a	38.203 Å
Unit-cell length b length_b	38.203 Å
Unit-cell length c length_c	263.349 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	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	0.2576
R_work r_work	0.2558
R_free r_free	0.2939

Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist

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

Abscisic acid receptor PYR1

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

5ygv__assembly_1__model_1

5ygv__assembly_1__model_1 | I(q)

5ygv__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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist

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

Abscisic acid receptor PYR1

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

5ygv__assembly_1__model_1

5ygv__assembly_1__model_1 | I(q)

5ygv__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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)