MolNFT v1 · #145613 · protein + DNA

Structure of the human cgas-DNA complex

6CT9 · Cyclic gmp-AMP synthase: “Structure of the human cgas-DNA complex”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.74). MolNFT v1 #145613 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6CT9
Type: protein + DNA
Length: 377 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: ZN
Pockets: 4 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic gmp-AMP synthase (EC 2.7.7.86)	protein	348	45% 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

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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	95	0.74	0.96	16	empty
2	603	0.71	0.79	54	empty
3	911	0.71	0.76	54	empty
4	290	0.59	0.78	26	empty

Interfaces

3 interfaces between chains.

B–C · 613 Å² buried · 69 hydrogen bonds · nucleic-nucleic
A–C · 484 Å² buried · 7 hydrogen bonds · protein-nucleic
A–B · 352 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

6CT9 · Structure of the human cGAS-DNA complex · 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 6CT9 · PDBe 6CT9 · UniProt Q8N884

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