Research workbench
Crystal structure of tRNA adenosine deaminase from bacillus subtilis
Analyse Crystal structure of tRNA adenosine deaminase from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CPH
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-specific adenosine deaminase
- EC
- 3.5.4.33
- UniProt
- P21335
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-specific adenosine deaminase (EC 3.5.4.33) | protein | 152 | 39% helix, 20% strand | P21335 |
| B | TRNA-specific adenosine deaminase (EC 3.5.4.33) | protein | 156 | 40% helix, 19% strand | P21335 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.70 | 0.84 | 33 | GOL |
| 2 | 275 | 0.59 | 0.78 | 33 | empty |
| 3 | 58 | 0.35 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1358 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7CPH · Crystal structure of tRNA adenosine deaminase from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P21335 · AlphaFold monomer V2.0 prediction for tRNA-specific adenosine deaminase (P21335) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P21335
- Elsewhere: RCSB PDB 7CPH · PDBe 7CPH · UniProt P21335
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