Research workbench
Human cyclic gmp-AMP synthase (cgas) in complex with compound F1
Analyse Human cyclic gmp-AMP synthase (cgas) in complex with compound F1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VDW
- 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
- 9BY, ZN
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclic gmp-AMP synthase (EC 2.7.7.86) | protein | 360 | 42% helix, 18% strand | Q8N884 |
Ligands and binding sites
- 9BY · [2-(1,3-thiazol-4-yl)-1H-benzimidazol-1-yl]acetic acid · ligand · 2 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.75 | 0.78 | 90 | 9BY |
| 2 | 755 | 0.73 | 0.78 | 74 | 9BY |
| 3 | 296 | 0.62 | 0.79 | 30 | empty |
| 4 | 145 | 0.47 | 0.77 | 26 | empty |
| 5 | 75 | 0.41 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 707 Ų buried · 17 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 5VDW · PDBe 5VDW · UniProt Q8N884
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