6YWA | pdb_00006ywa

Human REF STING in complex with 3',3'-c-[2'FdAMP-2'FdAM(PS)]

PDB DOI: https://doi.org/10.2210/pdb6YWA/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-29 Released: 2021-05-12
Deposition Author(s): Boura, E., Smola, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.244 (Depositor), 0.244 (DCC)
R-Value Work:
0.194 (Depositor), 0.196 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6YWA

Ligand Structure Quality Assessment

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

Literature

Human REF STING in complex with 3',3'-c-[2'FdAMP-2'FdAM(PS)]

Boura, E., Smola, M.

To be published.

Macromolecule Content

Total Structure Weight: 47.11 kDa
Atom Count: 3,127
Modeled Residue Count: 364
Deposited Residue Count: 408
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, B	204	Homo sapiens	Mutation(s): 0 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PWB (Subject of Investigation/LOI) Query on PWB Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	3',3'-c-[2'FdAMP-2'FdAM(PS)] C₂₀ H₂₄ F₂ N₁₀ O₉ P₂ S ACFLUKTZBKNITE-VIORMFSVSA-P		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.244 (Depositor), 0.244 (DCC)
R-Value Work: 0.194 (Depositor), 0.196 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.959	α = 90
b = 94.244	β = 90
c = 116.826	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-05-12
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.