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The structure of the N-terminal doamin of the schizosaccharomyces pombe TAD2 adenosine deaminase
Analyse The structure of the N-terminal doamin of the schizosaccharomyces pombe TAD2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EEY
- Type
- protein
- Length
- 778 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-specific adenosine deaminase subunit TAD2
- EC
- 3.5.4.33
- UniProt
- O94642
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-specific adenosine deaminase subunit TAD2 (EC 3.5.4.33) | protein | 193 | 51% helix, 20% strand | O94642 |
| B | TRNA-specific adenosine deaminase subunit TAD2 (EC 3.5.4.33) | protein | 194 | 52% helix, 20% strand | O94642 |
| C | TRNA-specific adenosine deaminase subunit TAD2 (EC 3.5.4.33) | protein | 195 | 51% helix, 20% strand | O94642 |
| D | TRNA-specific adenosine deaminase subunit TAD2 (EC 3.5.4.33) | protein | 196 | 51% helix, 20% strand | O94642 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.84 | 0.84 | 97 | SO4 |
| 2 | 1124 | 0.73 | 0.76 | 96 | SO4 |
| 3 | 111 | 0.45 | 0.78 | 27 | empty |
| 4 | 118 | 0.44 | 0.77 | 24 | empty |
| 5 | 51 | 0.41 | 0.82 | 11 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1121 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 858 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7EEY · The structure of the N-terminal doamin of the Schizosaccharomyces pombe Tad2 adenosine… · the same entry in another collection · chain D against D, TM-score 1.00
- O94642 · AlphaFold monomer V2.0 prediction for tRNA-specific adenosine deaminase subunit TAD2… · a predicted model of the same protein · chain C 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 O94642
- Elsewhere: RCSB PDB 7EEY · PDBe 7EEY · UniProt O94642
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