SAXSdb — 7vnh

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

Ahr homolog spineless

Drosophila melanogaster

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 264–381	Not recorded	BHF 2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris-HCl pH 7.0, 0.2 M NaCl, 0.8 M sodium citrate	Resolution 2.40 Å R-free 0.268
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 264–381	Not recorded	BHF 2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris-HCl pH 7.0, 0.2 M NaCl, 0.8 M sodium citrate	Resolution 2.40 Å R-free 0.268

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7VNH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7VNA drosophlia AHR PAS-B domain Deposited 2021-10-10	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 264–381（118 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris-HCl pH 7.0, 0.2 M NaCl, 0.8 M sodium citrate	Resolution 2.60 Å R-free 0.250
7VNI AHR-ARNT PAS-B heterodimer Deposited 2021-10-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 264–381（118 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium arsenate (pH 6.5), 0.2 M MgCl2, 2 M (NH4)2SO4	Resolution 2.00 Å R-free 0.219
7VNI AHR-ARNT PAS-B heterodimer Deposited 2021-10-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 264–381（118 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium arsenate (pH 6.5), 0.2 M MgCl2, 2 M (NH4)2SO4	Resolution 2.00 Å R-free 0.219

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O61543_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–120； UniProt 264–381 Author chain B； PDBConstruct 3–120； UniProt 264–381

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	7vnh
Deposition date deposition_date	2021-10-11
Structure title title	drosophlia AHR PAS-B domain bound by the antagonist alpha-naphthoflavone
Keywords keywords	transcription factor, ligand binding domain, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.20 Å
Radius of gyration Rg (electron density) rg_electron	18.02 Å
Forward intensity I(0) i0	12279500.00
Molecular weight molecular_weight	26101.0 kDa
Excluded volume excluded_volume	32591 Å³
Envelope volume envelope_volume	37545 Å³
Hydration-shell volume shell_volume	17659 Å³
Envelope diameter envelope_diameter	64.5 Å
Shell Rg shell_rg	23.93 Å
Envelope Rg envelope_rg	18.28 Å
Shape Rg shape_rg	17.96 Å
Total Rg total_rg	19.10 Å
Total atoms total_atoms	1840
Residues n_residues	225
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	62.9 Å
Rg (real space) rg_real	19.17 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.2280e+07
I(0) uncertainty (real space) i0_real_error	1.4770e+05
Rg (reciprocal space) rg_reciprocal	19.17 Å
I(0) (reciprocal space) i0_reciprocal	12280000.0000
Solution quality estimate total_estimate	0.8820
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.7 Å
Skewness Skewness skewness	0.340
Kurtosis Kurtosis kurtosis	-0.279
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3783000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ahr homolog spineless
Molecular weight formula_weight	13811.7 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	1886

GSIPHKENMFKSKHKLDFSLVSMDQRGKHILGYADAELVNMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRYQKKDGEWQWLQTSSRLVYKNSKPDFVICTHRQLMDEEGHDLLGKR

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	Fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE
Molecular weight formula_weight	272.3 kDa
Source method src_method	nat
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	46

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8. Citations (1)

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Unit-cell length a length_a	60.235 Å
Unit-cell length b length_b	60.235 Å
Unit-cell length c length_c	121.046 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.402 Å
Low-resolution limit resolution_low	30.262 Å
R factor r_factor	0.2347
R_work r_work	0.2310
R_free r_free	0.2677

fit	/app/data/saxs_computation/vn/7vnh/7vnh.fit
pddf	/app/data/pr_computation/vn/7vnh/7vnh.pr.out
profile	/app/data/saxs_computation/vn/7vnh/7vnh.dat

drosophlia AHR PAS-B domain bound by the antagonist alpha-naphthoflavone

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

Ahr homolog spineless

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction