Research workbench
Crystal structure of tRNA adenosine deaminase tada from escherichia COLI
Analyse Crystal structure of tRNA adenosine deaminase tada from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z3A
- Type
- protein
- Length
- 312 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-specific adenosine deaminase
- EC
- 3.5.4.-
- UniProt
- P68398
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA-specific adenosine deaminase (EC 3.5.4.-) | protein | 156 | 38% helix, 19% strand | P68398 |
Ligands and binding sites
- 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
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 | 315 | 0.64 | 0.80 | 32 | empty |
| 2 | 307 | 0.63 | 0.79 | 40 | empty |
| 3 | 56 | 0.41 | 0.82 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1343 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1Z3A · Crystal structure of tRNA adenosine deaminase TadA from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
- P68398 · AlphaFold monomer V2.0 prediction for tRNA-specific adenosine deaminase (P68398) · 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 P68398
- Elsewhere: RCSB PDB 1Z3A · PDBe 1Z3A · UniProt P68398
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