7OB3 | pdb_00007ob3

hSTING in complex with 3',3'-c-di-araAMP

PDB DOI: https://doi.org/10.2210/pdb7OB3/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-04-20 Released: 2022-05-04
Deposition Author(s): Smola, M., Boura, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.230 (Depositor), 0.234 (DCC)
R-Value Work:
0.214 (Depositor), 0.215 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Enzymatic Synthesis of 3'-5', 3'-5' Cyclic Dinucleotides, Their Binding Properties to the Stimulator of Interferon Genes Adaptor Protein, and Structure/Activity Correlations

Novotna, B., Hola, L., Stas, M., Gutten, O., Smola, M., Zavrel, M., Vavrina, Z., Budesinsky, M., Liboska, R., Chevrier, F., Dobias, J., Boura, E., Rulisek, L., Birkus, G.

(2021) Biochemistry

DOI: https://doi.org/10.1021/acs.biochem.1c00692

Macromolecule Content

Total Structure Weight: 23.85 kDa
Atom Count: 1,584
Modeled Residue Count: 179
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 genes protein	A	204	Homo sapiens	Mutation(s): 1 Gene Names: STING1, ERIS, MITA, TMEM173
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
V7E (Subject of Investigation/LOI) Query on V7E 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]	3',3'-c-di-araAMP C₂₀ H₂₄ N₁₀ O₁₂ P₂ PDXMFTWFFKBFIN-SVHUXIIHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.230 (Depositor), 0.234 (DCC)
R-Value Work: 0.214 (Depositor), 0.215 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.335	α = 90
b = 67.335	β = 90
c = 134.945	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-05-04
Type: Initial release
Version 1.1: 2023-11-15
Changes: Data collection, Database references
Version 1.2: 2024-01-31
Changes: Refinement description

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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.