MolNFT v1 · #145614 · protein + DNA

Structure of the human cgas-DNA complex with ATP

6CTA · Cyclic gmp-AMP synthase: “Structure of the human cgas-DNA complex with ATP”. X-ray diffraction, 3 ligands (ATP, MG, ZN), 4 pockets (best druggability 0.74). MolNFT v1 #145614 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6CTA
Type: protein + DNA
Length: 373 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic gmp-AMP synthase; DNA (5'-D(P*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*T)-3'); DNA…
EC: 2.7.7.86
UniProt: Q8N884
Ligands: ATP, MG, ZN
Pockets: 4 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic gmp-AMP synthase (EC 2.7.7.86)	protein	344	47% helix, 18% strand	Q8N884
B	DNA (5'-D(PCPGPTPCPTPTPCPGPGPCPAPAP*T)-3')	dna	13	—	—
C	DNA (5'-D(APAPAPTPTPGPCPCPGPAPAPGPAPCPGPA)- 3')	dna	16	—	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A
ZN · Zinc ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	956	0.74	0.78	65	empty
2	492	0.71	0.80	48	MG, ATP
3	302	0.62	0.79	27	empty
4	54	0.32	0.77	12	empty

Interfaces

3 interfaces between chains.

B–C · 615 Å² buried · 58 hydrogen bonds · nucleic-nucleic
A–C · 475 Å² buried · 6 hydrogen bonds · protein-nucleic
A–B · 349 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

6CTA · Structure of the human cGAS-DNA complex with ATP · the same entry in another collection · chain A against A, TM-score 1.00
Q8N884 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q8N884) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8N884
Elsewhere: RCSB PDB 6CTA · PDBe 6CTA · UniProt Q8N884

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