MolNFT v1 · #101922 · protein + DNA

Mouse cyclic gmp-AMP synthase (cgas) in complex with DNA

4O6A: “Mouse cyclic gmp-AMP synthase (cgas) in complex with DNA”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.87). MolNFT v1 #101922 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4O6A
Type: protein + DNA
Length: 782 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic gmp-AMP synthase; DNA1; DNA2
EC: 2.7.7.86
UniProt: Q8C6L5
Ligands: ZN
Pockets: 11 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic gmp-AMP synthase (EC 2.7.7.86)	protein	361	43% helix, 17% strand	Q8C6L5
D	DNA1	dna	15	—	—
E	DNA2	dna	14	—	—
B	Cyclic gmp-AMP synthase (EC 2.7.7.86)	protein	358	43% helix, 18% strand	Q8C6L5
C	DNA1	dna	17	—	—
F	DNA2	dna	17	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1121	0.87	0.88	104	empty
2	735	0.71	0.77	54	empty
3	721	0.71	0.78	58	empty
4	668	0.67	0.76	35	empty
5	355	0.62	0.78	32	empty

Interfaces

11 interfaces between chains.

A–B · 876 Å² buried · 18 hydrogen bonds · protein-protein
C–F · 705 Å² buried · 58 hydrogen bonds · nucleic-nucleic
D–E · 652 Å² buried · 65 hydrogen bonds · nucleic-nucleic
B–C · 547 Å² buried · 6 hydrogen bonds · protein-nucleic
A–D · 482 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

4O6A · Mouse cyclic GMP-AMP synthase (cGAS) in complex with DNA · the same entry in another collection · chain F against F, 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 0.98

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 4O6A · PDBe 4O6A · UniProt Q8C6L5

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