MolNFT v1 · #128941 · protein
X-ray structure of a bacterial adenylyl cyclase soluble domain
5O5K · Adenylate cyclase: “X-ray structure of a bacterial adenylyl cyclase soluble domain”. X-ray diffraction, 3 ligands (ONM, MN, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #128941 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5O5K
- Type
- protein
- Length
- 2,376 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate cyclase
- EC
- 4.6.1.1
- UniProt
- X8CHM4
- Ligands
- ONM, MN, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, C, E, F, I, J, H, G, K | Adenylate cyclase (EC 4.6.1.1) | protein | 216 | 40% helix, 33% strand | X8CHM4 |
Ligands and binding sites
- ONM · 3'-O-(N-methylanthraniloyl)-guanosine-5'-triphosphate · ligand · 11 copies · chains A, B, D, C, E, F, I, J, H, G, K
- MN · Manganese (II) ion · metal · 22 copies · chains A, B, D, C, E, F, I, J, H, G, K
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, D, C, E, F, H, I, J, K, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.80 | 0.81 | 79 | MN, ONM |
| 2 | 1126 | 0.77 | 0.79 | 82 | ONM, MN |
| 3 | 1148 | 0.77 | 0.79 | 83 | ONM, MN |
| 4 | 1117 | 0.76 | 0.78 | 90 | MN, ONM |
| 5 | 1137 | 0.76 | 0.78 | 80 | ONM, MN |
Interfaces
22 interfaces between chains.
- I–J · 2810 Ų buried · 37 hydrogen bonds · protein-protein
- H–G · 2703 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2700 Ų buried · 37 hydrogen bonds · protein-protein
- D–C · 2682 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2678 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5O5K · X-ray structure of a bacterial adenylyl cyclase soluble domain · the same entry in another collection · chain A against A, TM-score 1.00
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 X8CHM4
- Elsewhere: RCSB PDB 5O5K · PDBe 5O5K · UniProt X8CHM4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.