MolNFT v1 · #183677 · protein
Crystal structure of mouse ADAT2/ADAT3 tRNA deamination complex V128L mutant
7NZ9 · TRNA-specific adenosine deaminase 2: “Crystal structure of mouse ADAT2/ADAT3 tRNA deamination complex V128L mutant”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.71). MolNFT v1 #183677 on GenesisL1: 3D structure…
- PDB
- 7NZ9
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-specific adenosine deaminase 2; Probable inactive tRNA-specific adenosine…
- EC
- 3.5.4.33
- UniProt
- Q6P6J0, Q6PAT0
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-specific adenosine deaminase 2 (EC 3.5.4.33) | protein | 161 | 42% helix, 20% strand | Q6P6J0 |
| B | Probable inactive tRNA-specific adenosine deaminase-like protein 3 | protein | 282 | 29% helix, 23% strand | Q6PAT0 |
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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.71 | 0.87 | 32 | empty |
| 2 | 76 | 0.50 | 0.84 | 14 | empty |
| 3 | 121 | 0.41 | 0.75 | 20 | empty |
| 4 | 77 | 0.35 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1255 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7NZ9 · Crystal structure of mouse ADAT2/ADAT3 tRNA deamination complex V128L mutant · the same entry in another collection · chain A against A, TM-score 1.00
- Q6P6J0 · AlphaFold monomer V2.0 prediction for tRNA-specific adenosine deaminase 2 (Q6P6J0) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q6PAT0 · AlphaFold monomer V2.0 prediction for probable inactive tRNA-specific adenosine… · a predicted model of the same protein · chain B against A, TM-score 0.63
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 Q6P6J0
- Every structure of UniProt Q6PAT0
- Elsewhere: RCSB PDB 7NZ9 · PDBe 7NZ9 · UniProt Q6P6J0 · UniProt Q6PAT0
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