9WHF | pdb_00009whf

Crystal Structure of Duck STING bound to diABZI3

PDB DOI: https://doi.org/10.2210/pdb9WHF/pdb

Classification: SIGNALING PROTEIN
Organism(s): Anas platyrhynchos
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-26 Released: 2026-03-04
Deposition Author(s): Zhao, Z.Z., Li, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.215 (Depositor), 0.217 (DCC)
R-Value Work:
0.194 (Depositor), 0.196 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Species-Specific Regulation of STING by a C195 Disulfide Tetramer in Duck

Zhao, Z.Z., Li, X.

To be published.

Macromolecule Content

Total Structure Weight: 22.89 kDa
Atom Count: 1,732
Modeled Residue Count: 180
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon genes protein	A	188	Anas platyrhynchos	Mutation(s): 0
UniProt
Find proteins for A0A8B9TBW9 (Anas platyrhynchos) Explore A0A8B9TBW9 Go to UniProtKB: A0A8B9TBW9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8B9TBW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AZ0 (Subject of Investigation/LOI) Query on A1AZ0 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]	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 C₄₂ H₅₁ N₁₃ O₇ JGLMVXWAHNTPRF-CMDGGOBGSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.215 (Depositor), 0.217 (DCC)
R-Value Work: 0.194 (Depositor), 0.196 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.05	α = 90
b = 67.05	β = 90
c = 98.07	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32373020

Revision History (Full details and data files)

Version 1.0: 2026-03-04
Type: Initial release

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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.