SAXSdb — 9o42

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

Pregnane X receptor ligand binding domain tethered to steroid receptor coactivator-1 peptide

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	(1P)-N-(5-tert-butyl-2-{[(3S)-hexan-3-yl]oxy}phenyl)-1-(2,4-dimethoxy-5-methylphenyl)-5-methyl-1H-1,2,3-triazole-4-carboxamide × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NR1I2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–316； UniProt 130–434 Author chain B； PDBConstruct 12–316； UniProt 130–434

Pregnane X receptor ligand binding domain tethered to steroid receptor coactivator-1 peptide

Homo sapiens

UniProt Q15788

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	(1P)-N-(5-tert-butyl-2-{[(3S)-hexan-3-yl]oxy}phenyl)-1-(2,4-dimethoxy-5-methylphenyl)-5-methyl-1H-1,2,3-triazole-4-carboxamide × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCOA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 327–355； UniProt 682–710 Author chain B； PDBConstruct 327–355； UniProt 682–710

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	9o42
Deposition date deposition_date	2025-04-08
Structure title title	Crystal structure of the L411A mutant of pregnane X receptor ligand binding domain in complex with SJPYT-328
Keywords keywords	Pregnane X receptor, PXR, NR1I2, transcription factor, nuclear receptor, drug metabolism, TRANSCRIPTION; TRANSCRIPTION
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.

9o42__assembly_1__model_1

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

Download this curve (.dat)

9o42__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9o42__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.87 Å
Rg (electron density)	32.94 Å
Total Rg	33.45 Å
Atom count	4632
Residues	579
Excluded volume	83068 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9o42__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	Pregnane X receptor ligand binding domain tethered to steroid receptor coactivator-1 peptide
Molecular weight formula_weight	40300.2 kDa
EC 编号 ec_number	2.3.1.48
Mutation mutation	L411A
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	4724

MKKGHHHHHHGSERTGTQPLGVQGLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRALRIQDIHPFATPLMQELFGITGSSGGSGGSSHSSLTERHKILHRLLQEGSPSDITTLSVEPD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(1P)-N-(5-tert-butyl-2-{[(3S)-hexan-3-yl]oxy}phenyl)-1-(2,4-dimethoxy-5-methylphenyl)-5-methyl-1H-1,2,3-triazole-4-carboxamide
Molecular weight formula_weight	508.7 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	80

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Unit-cell length a length_a	85.440 Å
Unit-cell length b length_b	89.909 Å
Unit-cell length c length_c	106.293 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.510 Å
Low-resolution limit resolution_low	45.750 Å
R factor r_factor	0.1996
R_work r_work	0.1985
R_free r_free	0.2186

Crystal structure of the L411A mutant of pregnane X receptor ligand binding domain in complex with SJPYT-328

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

Pregnane X receptor ligand binding domain tethered to steroid receptor coactivator-1 peptide

State in the Current Structure

Other States of the Same Protein in the Database

Pregnane X receptor ligand binding domain tethered to steroid receptor coactivator-1 peptide

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

9o42__assembly_1__model_1

9o42__assembly_1__model_1 | I(q)

9o42__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

7. Citations (1)

Crystal structure of the L411A mutant of pregnane X receptor ligand binding domain in complex with SJPYT-328

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

Pregnane X receptor ligand binding domain tethered to steroid receptor coactivator-1 peptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pregnane X receptor ligand binding domain tethered to steroid receptor coactivator-1 peptide

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

9o42__assembly_1__model_1

9o42__assembly_1__model_1 | I(q)

9o42__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

7. Citations (1)