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9qvt

Crystal structure of STING CTD in complex with potent agonist D5

Method: X-RAY DIFFRACTION D_max: 58.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qvt
deposition_date	2025-04-11
title	Crystal structure of STING CTD in complex with potent agonist D5
keywords	STING, Immune System, cGAS, agonist, interferon, signalling, SIGNALING PROTEIN; SIGNALING PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	17.59 Å
rg_electron	16.58 Å
i0	12848200.00
molecular_weight	17529.0 kDa
excluded_volume	16736 Å³
envelope_volume	28777 Å³
shell_volume	14894 Å³
envelope_diameter	58.8 Å
shell_rg	22.12 Å
envelope_rg	16.84 Å
shape_rg	16.56 Å
total_rg	17.34 Å
total_atoms	1322
n_residues	182
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	58.9 Å
rg_real	17.51 Å
rg_real_error	0.37 Å
i0_real	1.2850e+07
i0_real_error	1.4400e+05
rg_reciprocal	17.52 Å
i0_reciprocal	12850000.0000
total_estimate	0.7817
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	23.6 Å
skewness	0.228
kurtosis	-0.320
angular_range	— – 0.4500 Å⁻¹
current_alpha	0.0000
highest_alpha	2535000.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 0.983; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Stimulator of interferon genes protein
formula_weight	27154.6 kDa
mutation	L139S,H232R
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1349

GSAPAEISAVCEKGNFNVAHGLAWSYYIGYLRLILPELQARIRTYNQHYNNLLRGAVSQRLYILLPLDCGVPDNLSMADPNIRFLDKLPQQTGDRAGIKDRVYSNSIYELLENGQRAGTCVLEYATPLQTLFAMSQYSQAGFSREDRLEQAKLFCRTLEDILADAPESQNNCRLIAYQEPADDSSFSLSQEVLRHLRQEEKEEVTVGSLKTSAVPSTSTMSQEPELLISGMEKPLPLRTDFS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	;4-[6-methoxy-5-[[6-methoxy-2-(4-oxidanyl-4-oxidanylidene-butanoyl)-1-benzothiophen-5-yl]sulfanylmethylsulfanyl]-1-benzothiophen-2-yl]-4-oxidanylidene-butanoic acid ;
formula_weight	604.7 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	27

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6. Citations (1)

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length_a	89.681 Å
length_b	75.595 Å
length_c	34.138 Å
angle_alpha	90.00 °
angle_beta	97.75 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.305 Å
resolution_low	57.579 Å
r_factor	—
r_work	0.3422
r_free	0.3881

fit	/app/data/saxs_computation/qv/9qvt/9qvt.fit
pddf	/app/data/pr_computation/qv/9qvt/9qvt.pr.out
profile	/app/data/saxs_computation/qv/9qvt/9qvt.dat

Crystal structure of STING CTD in complex with potent agonist D5

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction