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- PDB-9ijn: STING LBD domain with an agonist DW18343 -

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Basic information

Entry
Database: PDB / ID: 9ijn
TitleSTING LBD domain with an agonist DW18343
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / STING LBD domain / Agonist
Function / homology
Function and homology information


autophagosome membrane / positive regulation of type I interferon production / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / mitochondrial outer membrane / nucleotide binding / perinuclear region of cytoplasm
Similarity search - Function
: / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain
Similarity search - Domain/homology
: / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsWang, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: MedComm (2020) / Year: 2025
Title: Discovery of a non-nucleotide stimulator of interferon genes (STING) agonist with systemic antitumor effect.
Authors: Wang, X. / Zhan, Z. / Wang, Z. / Zhang, Y. / Zhao, K. / Li, H. / Zhou, X. / Guo, Y. / Fan, F. / Ding, J. / Geng, M. / Yu, X. / Duan, W. / Xie, Z.
History
DepositionJun 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8882
Polymers21,5701
Non-polymers3171
Water2,126118
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7754
Polymers43,1402
Non-polymers6352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4010 Å2
ΔGint-18 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.040, 110.040, 35.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-566-

HOH

21A-587-

HOH

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Components

#1: Protein Stimulator of interferon genes protein


Mass: 21570.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING, LOC340061, hCG_1782396 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R3XZB7
#2: Chemical ChemComp-A1D9I / 4-[4-(7-fluoranyl-1H-indol-3-yl)thiophen-2-yl]-4-oxidanylidene-butanoic acid / SCHEMBL23330381


Mass: 317.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12FNO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 20% w/v Polyethylene glycol monomethyl ether 5,000 and 0.1 M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.81→34.8 Å / Num. obs: 20598 / % possible obs: 99.87 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.5
Reflection shellResolution: 1.81→1.86 Å / Rmerge(I) obs: 0.468 / Num. unique obs: 2713

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→34.8 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 995 4.83 %
Rwork0.1966 --
obs0.1984 20598 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1412 0 22 118 1552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131463
X-RAY DIFFRACTIONf_angle_d1.3911983
X-RAY DIFFRACTIONf_dihedral_angle_d13.638213
X-RAY DIFFRACTIONf_chiral_restr0.067214
X-RAY DIFFRACTIONf_plane_restr0.008262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.910.29411550.29212713X-RAY DIFFRACTION100
1.91-2.020.29721320.24012747X-RAY DIFFRACTION100
2.02-2.180.23451460.20522747X-RAY DIFFRACTION100
2.18-2.40.22271350.18262792X-RAY DIFFRACTION100
2.4-2.750.22221420.17842792X-RAY DIFFRACTION100
2.75-3.460.23651350.1912823X-RAY DIFFRACTION100
3.46-34.80.21921500.19132989X-RAY DIFFRACTION100

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