Research workbench
Crystal structure of human tRNA-specific adenosine-34 deaminase subunit ADAT2
Analyse Crystal structure of human tRNA-specific adenosine-34 deaminase subunit ADAT2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DH1
- Type
- protein
- Length
- 643 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-specific adenosine deaminase 2
- EC
- 3.5.4.-
- UniProt
- Q7Z6V5
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-specific adenosine deaminase 2 (EC 3.5.4.-) | protein | 162 | 41% helix, 20% strand | Q7Z6V5 |
| B, C | TRNA-specific adenosine deaminase 2 (EC 3.5.4.-) | protein | 160 | 41% helix, 21% strand | Q7Z6V5 |
| D | TRNA-specific adenosine deaminase 2 (EC 3.5.4.-) | protein | 161 | 41% helix, 20% strand | Q7Z6V5 |
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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.67 | 0.81 | 38 | empty |
| 2 | 329 | 0.66 | 0.81 | 36 | empty |
| 3 | 347 | 0.66 | 0.80 | 38 | empty |
| 4 | 341 | 0.64 | 0.79 | 37 | empty |
| 5 | 238 | 0.63 | 0.82 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1223 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1128 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 1123 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3DH1 · Crystal structure of human tRNA-specific adenosine-34 deaminase subunit ADAT2 · the same entry in another collection · chain D against D, TM-score 1.00
- Q7Z6V5 · AlphaFold monomer V2.0 prediction for tRNA-specific adenosine deaminase 2 (Q7Z6V5) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q7Z6V5
- Elsewhere: RCSB PDB 3DH1 · PDBe 3DH1 · UniProt Q7Z6V5
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