MolNFT v1 · #140079 · protein + DNA

Mouse cgas bound to the inhibitor RU365

5XZB · Cyclic gmp-AMP synthase: “Mouse cgas bound to the inhibitor RU365”. X-ray diffraction, 2 ligands (A9Y, ZN), 5 pockets (best druggability 0.76). MolNFT v1 #140079 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XZB
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: A9Y, ZN
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic gmp-AMP synthase (EC 2.7.7.86)	protein	357	42% 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

A9Y · (3R)-3-[1-(1H-benzimidazol-2-yl)-5-hydroxy-3-methyl-1H-pyrazol-4-yl]-2-benzofuran-1(3H)-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

5 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	125	0.76	0.95	19	empty
2	781	0.73	0.78	69	A9Y
3	685	0.66	0.75	52	empty
4	337	0.57	0.76	30	empty
5	51	0.29	0.75	13	empty

Interfaces

3 interfaces between chains.

E–F · 659 Å² buried · 59 hydrogen bonds · nucleic-nucleic
A–E · 448 Å² buried · 7 hydrogen bonds · protein-nucleic
A–F · 290 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

5XZB · Mouse cGAS bound to the inhibitor RU365 · 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 5XZB · PDBe 5XZB · UniProt Q8C6L5

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