MolNFT v1 · #137095 · protein
Human cyclic gmp-AMP synthase (cgas) in complex with 2',2'-cgamp
5VDO: “Human cyclic gmp-AMP synthase (cgas) in complex with 2',2'-cgamp”. X-ray diffraction, 2 ligands (1YC, ZN), 9 pockets (best druggability 0.75). MolNFT v1 #137095 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VDO
- Type
- protein
- Length
- 715 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
- 1YC, ZN
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic gmp-AMP synthase (EC 2.7.7.86) | protein | 360 | 43% helix, 17% strand | Q8N884 |
| B | Cyclic gmp-AMP synthase (EC 2.7.7.86) | protein | 355 | 44% helix, 18% strand | Q8N884 |
Ligands and binding sites
- 1YC · 2-amino-9-[(1R,3R,6R,8R,9R,11S,14R,16R,17R,18R)-16-(6-amino-9H-purin-9-yl)-3,11,17,18-tetrahydroxy-3,11-dioxido-2,4,7,10,12,15-hexaoxa-3,11-diphosphatricyclo[12.2.1.1~6,9~]octadec-8-yl]-1,9-dihydro-6H-purin-6-one · 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.75 | 0.77 | 81 | 1YC |
| 2 | 956 | 0.71 | 0.75 | 72 | 1YC |
| 3 | 331 | 0.59 | 0.77 | 39 | empty |
| 4 | 51 | 0.48 | 0.86 | 15 | empty |
| 5 | 89 | 0.43 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 736 Ų buried · 13 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 5VDO · PDBe 5VDO · UniProt Q8N884
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