MolNFT v1 · #151702 · protein
Cdaa complex with C-di-AMP and AMP
6HVL · Diadenylate cyclase: “Cdaa complex with C-di-AMP and AMP”. X-ray diffraction, 4 ligands (2BA, AMP, CO), 2 pockets (best druggability 0.37). MolNFT v1 #151702 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HVL
- Type
- protein
- Length
- 312 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diadenylate cyclase
- EC
- 2.7.7.85
- UniProt
- Q8Y5E4
- Ligands
- 2BA, AMP, CO, PO4
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diadenylate cyclase (EC 2.7.7.85) | protein | 158 | 36% helix, 23% strand | Q8Y5E4 |
| B | Diadenylate cyclase (EC 2.7.7.85) | protein | 154 | 38% helix, 25% strand | Q8Y5E4 |
Ligands and binding sites
- 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains B
- CO · Cobalt (II) ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.37 | 0.77 | 15 | empty |
| 2 | 63 | 0.33 | 0.76 | 20 | AMP |
Interfaces
1 interface between chains.
- A–B · 756 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 Q8Y5E4
- Elsewhere: RCSB PDB 6HVL · PDBe 6HVL · UniProt Q8Y5E4
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