MolNFT v1 · #137098 · protein
Human cyclic gmp-AMP synthase (cgas) in complex with 3',3'-cdimp
5VDR: “Human cyclic gmp-AMP synthase (cgas) in complex with 3',3'-cdimp”. X-ray diffraction, 2 ligands (9B7, ZN), 7 pockets (best druggability 0.76). MolNFT v1 #137098 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VDR
- Type
- protein
- Length
- 710 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
- 9B7, ZN
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 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
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 | 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 Ų buried · 15 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 5VDR · PDBe 5VDR · UniProt Q8N884
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