8A2X | pdb_00008a2x

Crystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP(S)-2'F,2'd<carba>AMP(S))

PDB DOI: https://doi.org/10.2210/pdb8A2X/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-06 Released: 2023-12-20
Deposition Author(s): Klima, M., Smola, M., Boura, E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.291 (Depositor), 0.291 (DCC)
R-Value Work:
0.222 (Depositor), 0.222 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP(S)-2'F,2'dAMP(S))

Klima, M., Smola, M., Boura, E.

To be published.

Macromolecule Content

Total Structure Weight: 23.88 kDa
Atom Count: 1,453
Modeled Residue Count: 175
Deposited Residue Count: 204
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon protein	A	204	Homo sapiens	Mutation(s): 0 Gene Names: STING, LOC340061, hCG_1782396
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WV6 (Homo sapiens) Explore Q86WV6 Go to UniProtKB: Q86WV6
PHAROS: Q86WV6 GTEx: ENSG00000184584
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86WV6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KZA (Subject of Investigation/LOI) Query on KZA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	9-[(1~{R},3~{R},6~{R},8~{R},9~{R},10~{R},12~{R},15~{R},17~{R},18~{S})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanylidene)-3,12-bis(sulfanyl)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-17-yl]purin-6-amine C₂₁ H₂₄ F₂ N₁₀ O₇ P₂ S₂ TYYDPOXHOPCCQR-SWACTAJXSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.291 (Depositor), 0.291 (DCC)
R-Value Work: 0.222 (Depositor), 0.222 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.009	α = 90
b = 111.009	β = 90
c = 35.625	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-12-20
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.