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Human cyclic GMP-AMP synthase (cGAS) in complex with 3',3'-cdIMP

Analyse Human cyclic GMP-AMP synthase (cGAS) in complex with 3',3'-cdIMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VDR
Type: protein
Length: 710 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.042
Source: Homo sapiens
Molecule: Cyclic GMP-AMP synthase
EC: 2.7.7.86
UniProt: Q8N884
Ligands: 9B7, ZN
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · resolution 3.042 · 2 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic GMP-AMP synthase (EC 2.7.7.86)	protein	357	44% helix, 17% strand	Q8N884
B	Cyclic GMP-AMP synthase (EC 2.7.7.86)	protein	353	44% helix, 19% strand	Q8N884

Ligands and binding sites

9B7 · 3',3'-cdIMP · ligand · 4 copies · chains A, B
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

7 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	1062	0.76	0.78	75	9B7
2	845	0.70	0.75	66	9B7
3	240	0.58	0.79	27	empty
4	67	0.37	0.78	16	empty
5	84	0.33	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 712 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5VDR · Human cyclic gmp-AMP synthase (cgas) in complex with 3',3'-cdimp · 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 B 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 Q8N884
Elsewhere: RCSB PDB 5VDR · PDBe 5VDR · UniProt Q8N884

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