MolNFT v1 · #26685 · protein
Crystal structure of tRNA adenosine deaminase tada from aquifex aeolicus
1WWR: “Crystal structure of tRNA adenosine deaminase tada from aquifex aeolicus”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.72). MolNFT v1 #26685 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1WWR
- Type
- protein
- Length
- 622 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA adenosine deaminase tada
- EC
- 3.5.4.-
- UniProt
- O67050
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA adenosine deaminase tada (EC 3.5.4.-) | protein | 154 | 40% helix, 18% strand | O67050 |
| B | TRNA adenosine deaminase tada (EC 3.5.4.-) | protein | 157 | 38% helix, 18% strand | O67050 |
| C | TRNA adenosine deaminase tada (EC 3.5.4.-) | protein | 160 | 38% helix, 18% strand | O67050 |
| D | TRNA adenosine deaminase tada (EC 3.5.4.-) | protein | 151 | 41% helix, 19% strand | O67050 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.72 | 0.77 | 60 | empty |
| 2 | 292 | 0.65 | 0.81 | 36 | empty |
| 3 | 285 | 0.64 | 0.81 | 34 | empty |
| 4 | 63 | 0.57 | 0.89 | 24 | empty |
| 5 | 69 | 0.34 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1363 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1336 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 781 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 172 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 162 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1WWR · Crystal structure of tRNA adenosine deaminase TadA from Aquifex aeolicus · the same entry in another collection · chain D against D, TM-score 1.00
- O67050 · AlphaFold monomer V2.0 prediction for tRNA-specific adenosine deaminase (O67050) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 O67050
- Elsewhere: RCSB PDB 1WWR · PDBe 1WWR · UniProt O67050
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