MolNFT v1 · #97285 · protein + DNA

Structure of ternary complex of cgas with dsdna and bound ATP

4K97 · Cyclic gmp-AMP synthase: “Structure of ternary complex of cgas with dsdna and bound ATP”. X-ray diffraction, 3 ligands (ATP, MG, ZN), 3 pockets (best druggability 0.74). MolNFT v1 #97285 on GenesisL1: 3D structure, binding sites and…

PDB: 4K97
Type: protein + DNA
Length: 380 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic gmp-AMP synthase; DNA-F; DNA-R
EC: 2.7.7.-
UniProt: Q8C6L5
Ligands: ATP, MG, ZN
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic gmp-AMP synthase (EC 2.7.7.-)	protein	351	40% helix, 18% strand	Q8C6L5
D	DNA-F	dna	15	—	—
E	DNA-R	dna	14	—	—

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

3 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	839	0.74	0.78	66	MG, ATP
2	798	0.72	0.78	57	empty
3	445	0.61	0.76	30	empty

Interfaces

3 interfaces between chains.

D–E · 637 Å² buried · 63 hydrogen bonds · nucleic-nucleic
A–D · 502 Å² buried · 6 hydrogen bonds · protein-nucleic
A–E · 300 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

4K97 · Structure of Ternary Complex of cGAS with dsDNA and Bound ATP · the same entry in another collection · chain A against A, TM-score 1.00
Q8C6L5 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q8C6L5) · 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 Q8C6L5
Elsewhere: RCSB PDB 4K97 · PDBe 4K97 · UniProt Q8C6L5

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