SAXSdb — 9wh9

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

Stimulator of interferon genes protein

Bos taurus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 155–340 Chain B； UniProt 155–340	Not recorded	A1AZ0 1-[(2E)-4-{5-carbamoyl-2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-7-methoxy-1H-1,3-benzimidazol-1-yl}but-2-en-1-yl]-2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-7-[3-(morpholin-4-yl)propoxy]-1H-1,3-benzimidazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；0.1M HEPES sodium pH7.5, 0.8M Sodium phosphate monobasic monohydrate, 0.8M Potassium phosphate monobasic	Resolution 1.81 Å R-free 0.258

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 9WH9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9WHA Crystal Structure of Bovine STING bound to 2'3'-cGAMP Deposited 2025-08-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 155–340（186 aa） Chain B 155–340（186 aa）	Not recorded	1SY cGAMP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Sodium acetate trihydrate pH4.6, 2M Sodium chloride	Resolution 1.60 Å R-free 0.241

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STING_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–187； UniProt 155–340 Author chain B； PDBConstruct 2–187； UniProt 155–340

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	9wh9
Deposition date deposition_date	2025-08-26
最后修订 last_revision	2026-03-04
Structure title title	Crystal Structure of Bovine STING bound to diABZI3
Keywords keywords	STING, diABZI3, SIGNALING PROTEIN; SIGNALING PROTEIN
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	23.76 Å
Radius of gyration Rg (electron density) rg_electron	22.75 Å
Forward intensity I(0) i0	55397900.00
Molecular weight molecular_weight	38354.0 kDa
Excluded volume excluded_volume	36896 Å³
Envelope volume envelope_volume	62947 Å³
Hydration-shell volume shell_volume	23383 Å³
Envelope diameter envelope_diameter	80.4 Å
Shell Rg shell_rg	29.58 Å
Envelope Rg envelope_rg	23.01 Å
Shape Rg shape_rg	22.71 Å
Total Rg total_rg	23.45 Å
Total atoms total_atoms	2908
Residues n_residues	356
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	77.0 Å
Rg (real space) rg_real	23.76 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	5.5400e+07
I(0) uncertainty (real space) i0_real_error	7.3690e+05
Rg (reciprocal space) rg_reciprocal	23.76 Å
I(0) (reciprocal space) i0_reciprocal	55400000.0000
Solution quality estimate total_estimate	0.8170
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.7 Å
Skewness Skewness skewness	0.348
Kurtosis Kurtosis kurtosis	-0.359
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8894000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.000

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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	Stimulator of interferon genes protein
Molecular weight formula_weight	22249.0 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	3032

MVAHGLAWSYYIGYLRLILPGLPARIQIYNQFHNNTLQGAGSHRLHILFPLDCGVPDDLNVADPNIRFLHELPQQSADRAGIKGRVYTNSIYELLENGQRAGVCVLEYATPLQTLFAMSQDGRAGFSREDRLEQAKLFCRTLEDILANAPESQNNCRLIVYQEPAEGSSFSLSQEILQHLRQEEREVLEHHHHHH

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	domestic cattle
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;1-[(2E)-4-{5-carbamoyl-2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-7-methoxy-1H-1,3-benzimidazol-1-yl}but-2-en-1-yl]-2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-7-[3-(morpholin-4-yl)propoxy]-1H-1,3-benzimidazole-5-carboxamide ;
Molecular weight formula_weight	849.9 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

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8. Citations (1)

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Unit-cell length a length_a	44.997 Å
Unit-cell length b length_b	57.544 Å
Unit-cell length c length_c	136.378 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	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	29.330 Å
R factor r_factor	0.2029
R_work r_work	0.1999
R_free r_free	0.2583

fit	/app/data/saxs_computation/wh/9wh9/9wh9.fit
pddf	/app/data/pr_computation/wh/9wh9/9wh9.pr.out
profile	/app/data/saxs_computation/wh/9wh9/9wh9.dat

Crystal Structure of Bovine STING bound to diABZI3

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

Stimulator of interferon genes protein

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