MolNFT v1 · #137096 · protein

Human cyclic gmp-AMP synthase (cgas) in complex with 2',3'-cgamp

5VDP: “Human cyclic gmp-AMP synthase (cgas) in complex with 2',3'-cgamp”. X-ray diffraction, 3 ligands (1SY, ZN, SO4), 6 pockets (best druggability 0.76). MolNFT v1 #137096 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VDP
Type: protein
Length: 720 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic gmp-AMP synthase
EC: 2.7.7.86
UniProt: Q8N884
Ligands: 1SY, ZN, SO4
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cyclic gmp-AMP synthase (EC 2.7.7.86)	protein	360	43% helix, 19% strand	Q8N884

Ligands and binding sites

1SY · cGAMP · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 5 copies · chains A, B

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

Pockets

6 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	1185	0.76	0.78	84	1SY
2	1178	0.75	0.77	83	1SY
3	199	0.56	0.79	23	empty
4	108	0.36	0.74	26	empty
5	64	0.36	0.78	17	empty

Interfaces

1 interface between chains.

A–B · 711 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

5VDP · Human cyclic GMP-AMP synthase (cGAS) in complex with 2',3'-cGAMP · 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 0.97

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 5VDP · PDBe 5VDP · UniProt Q8N884

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.