Research workbench
Human cyclic gmp-AMP synthase (cgas) in complex with compound F3
Analyse Human cyclic gmp-AMP synthase (cgas) in complex with compound F3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VDV
- Type
- protein
- Length
- 706 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
- 9BV, ZN, SO4
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic gmp-AMP synthase (EC 2.7.7.86) | protein | 357 | 45% helix, 18% strand | Q8N884 |
| B | Cyclic gmp-AMP synthase (EC 2.7.7.86) | protein | 349 | 45% helix, 17% strand | Q8N884 |
Ligands and binding sites
- 9BV · tetrazolo[5,1-b]quinazolin-9-ol · ligand · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.71 | 0.78 | 62 | 9BV |
| 2 | 629 | 0.71 | 0.78 | 69 | 9BV |
| 3 | 286 | 0.59 | 0.78 | 27 | empty |
| 4 | 278 | 0.54 | 0.76 | 36 | empty |
| 5 | 100 | 0.52 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 701 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
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 5VDV · PDBe 5VDV · UniProt Q8N884
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