MolNFT v1 · #140084 · protein + DNA

Mouse cgas bound to the inhibitor RU521

5XZG · Cyclic gmp-AMP synthase: “Mouse cgas bound to the inhibitor RU521”. X-ray diffraction, 2 ligands (AEV, ZN), 4 pockets (best druggability 0.74). MolNFT v1 #140084 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XZG
Type: protein + DNA
Length: 386 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic gmp-AMP synthase; DNA (5'-D(*AP*AP*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*G)- 3')…
EC: 2.7.7.86
UniProt: Q8C6L5
Ligands: AEV, ZN
Pockets: 4 · best druggability 0.74

Structure

x-ray diffraction · 3 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	357	43% helix, 18% strand	Q8C6L5
E	DNA (5'-D(APAPAPTPTPGPCPCPGPAPAPGPAPCP*G)- 3')	dna	15	—	—
F	DNA (5'-D(PCPGPTPCPTPTPCPGPGPCPAPAPTPT)-3')	dna	14	—	—

Ligands and binding sites

AEV · 2-(4,5-dichloro-1H-benzimidazol-2-yl)-5-methyl-4-[(1R)-3-oxo-1,3-dihydro-2-benzofuran-1-yl]-1,2-dihydro-3H-pyrazol-3-one · ligand · 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	869	0.74	0.78	74	AEV
2	362	0.70	0.83	39	empty
3	346	0.56	0.75	28	empty
4	283	0.49	0.73	21	empty

Interfaces

3 interfaces between chains.

E–F · 663 Å² buried · 62 hydrogen bonds · nucleic-nucleic
A–E · 426 Å² buried · 7 hydrogen bonds · protein-nucleic
A–F · 285 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

5XZG · Mouse cGAS bound to the inhibitor RU521 · 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 5XZG · PDBe 5XZG · UniProt Q8C6L5

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