5GRM | pdb_00005grm

Crystal structure of rat STING in complex with cyclic GMP-AMP with 2'5'and 3'5'phosphodiester linkage(2'3'-cGAMP)

PDB DOI: https://doi.org/10.2210/pdb5GRM/pdb

Classification: IMMUNE SYSTEM
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-11 Released: 2017-10-25
Deposition Author(s): Zhang, H., Han, M.J., Tao, J.L., Ye, Z.Y., Du, X.X., Deng, M.J., Zhang, X.Y., Li, L.F., Jiang, Z.F., Su, X.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.193 (Depositor), 0.199 (DCC)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of rat STING in complex with cyclic GMP-AMP with 2'5'and 3'5'phosphodiester linkage(2'3'-cGAMP)

Zhang, H., Han, M.J., Tao, J.L., Ye, Z.Y., Du, X.X., Deng, M.J., Zhang, X.Y., Li, L.F., Jiang, Z.F., Su, X.D.

To be published.

Macromolecule Content

Total Structure Weight: 48.55 kDa
Atom Count: 3,473
Modeled Residue Count: 378
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon genes protein	A, B	210	Rattus norvegicus	Mutation(s): 0 Gene Names: Tmem173, Sting
UniProt
Find proteins for F1M391 (Rattus norvegicus) Explore F1M391 Go to UniProtKB: F1M391
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F1M391
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1SY Query on 1SY Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	cGAMP C₂₀ H₂₄ N₁₀ O₁₃ P₂ XRILCFTWUCUKJR-INFSMZHSSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.193 (Depositor), 0.199 (DCC)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.181 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.2	α = 90
b = 77.2	β = 90
c = 152.1	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-10-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-10-25
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary