MolNFT v2 · #227303 · protein
cryoEM structure of CRISPR associated effector, CARF-Adenosine deaminase 1, Cad1, in apo form with ATP (Asymmetric sites).
9C6F · Adenosine deaminase domain-containing protein: “cryoEM structure of CRISPR associated effector, CARF-Adenosine deaminase 1, Cad1, in apo form with ATP…”. Electron microscopy at 3.6, 2 ligands (ATP, MG), 20 pockets (best druggability…
- PDB
- 9C6F
- Type
- protein
- Length
- 3,588 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Bacteroidales bacterium
- Molecule
- Adenosine deaminase domain-containing protein
- UniProt
- A0A3C0QUR5
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.6 · 1 distinct chain · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Adenosine deaminase domain-containing protein | protein | 598 | 43% helix, 14% strand | A0A3C0QUR5 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, E
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.86 | 0.87 | 100 | empty |
| 2 | 812 | 0.86 | 0.89 | 79 | empty |
| 3 | 1106 | 0.86 | 0.87 | 108 | empty |
| 4 | 569 | 0.81 | 0.87 | 73 | empty |
| 5 | 591 | 0.79 | 0.85 | 80 | empty |
Interfaces
12 interfaces between chains.
- E–F · 3419 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3310 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 3238 Ų buried · 31 hydrogen bonds · protein-protein
- A–F · 1017 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 984 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 A0A3C0QUR5
- Elsewhere: RCSB PDB 9C6F · PDBe 9C6F · UniProt A0A3C0QUR5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.