8ECC | pdb_00008ecc

Structure of Ternary Complex of cGAS with dsDNA and Bound 5-pppI(2,5)pA

PDB DOI: https://doi.org/10.2210/pdb8ECC/pdb
NAKB: 8ECC

Classification: TRANSFERASE/DNA
Organism(s): Mus musculus, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-09-01 Released: 2024-01-17
Deposition Author(s): Wu, S., Sohn, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.259 (Depositor), 0.265 (DCC)
R-Value Work:
0.222 (Depositor), 0.225 (DCC)
R-Value Observed:
0.224 (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

Structure of Ternary Complex of cGAS with dsDNA and Bound 5-pppI(2,5)pA

Wu, S., Sohn, J.

To be published.

Macromolecule Content

Total Structure Weight: 108.86 kDa
Atom Count: 7,313
Modeled Residue Count: 761
Deposited Residue Count: 800
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic GMP-AMP synthase	A, B [auth C]	364	Mus musculus	Mutation(s): 0 EC: 2.7.7.86
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C6L5 (Mus musculus) Explore Q8C6L5 Go to UniProtKB: Q8C6L5
IMPC: MGI:2442261
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8C6L5
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
Palindromic DNA18	C [auth E], D [auth F], E [auth I], F [auth J]	18	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VWX (Subject of Investigation/LOI) Query on VWX Download:Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	[[(2~{R},3~{R},4~{R},5~{R})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate C₂₀ H₂₇ N₉ O₂₀ P₄ SWVKSPSEHJCWAI-XPWFQUROSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth C] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C]	I [auth A], L [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Interactions & Density Focus chain I [auth A] Focus chain L [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain H [auth A]	H [auth A], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth C] Interactions & Density Focus chain H [auth A] Focus chain K [auth C]