Research workbench
Crystal structure of the yeast heterodimeric ADAT2/3
Analyse Crystal structure of the yeast heterodimeric ADAT2/3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BV5
- Type
- protein
- Length
- 1,061 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-specific adenosine deaminase subunit TAD2; TRNA-specific adenosine deaminase subunit…
- EC
- 3.5.4.33
- UniProt
- P47058, Q9URQ3
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-specific adenosine deaminase subunit TAD2 (EC 3.5.4.33) | protein | 234 | 48% helix, 15% strand | P47058 |
| B | TRNA-specific adenosine deaminase subunit TAD2 (EC 3.5.4.33) | protein | 233 | 47% helix, 14% strand | P47058 |
| C | TRNA-specific adenosine deaminase subunit TAD3 | protein | 284 | 35% helix, 12% strand | Q9URQ3 |
| D | TRNA-specific adenosine deaminase subunit TAD3 | protein | 310 | 31% helix, 19% strand | Q9URQ3 |
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
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.73 | 0.81 | 51 | empty |
| 2 | 520 | 0.66 | 0.77 | 49 | empty |
| 3 | 387 | 0.66 | 0.79 | 45 | empty |
| 4 | 424 | 0.64 | 0.78 | 42 | empty |
| 5 | 121 | 0.57 | 0.84 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1529 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1455 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 719 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7BV5 · Crystal structure of the yeast heterodimeric ADAT2/3 · the same entry in another collection · chain A against A, TM-score 1.00
- P47058 · AlphaFold monomer V2.0 prediction for tRNA-specific adenosine deaminase subunit TAD2… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9URQ3 · AlphaFold monomer V2.0 prediction for tRNA-specific adenosine deaminase subunit TAD3… · a predicted model of the same protein · chain C against A, TM-score 0.86
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 P47058
- Every structure of UniProt Q9URQ3
- Elsewhere: RCSB PDB 7BV5 · PDBe 7BV5 · UniProt P47058 · UniProt Q9URQ3
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