Research workbench
Structure of selenomethionine substituted bifunctional dapa aminotransferase-dethiobiotin synthetase from arabidopsis thaliana in its apo form.
Analyse Structure of selenomethionine substituted bifunctional dapa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A0F
- Type
- protein
- Length
- 1,496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
- UniProt
- B0F481
- Ligands
- PLP, SO4
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | protein | 746 | 37% helix, 21% strand | B0F481 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | protein | 750 | 37% helix, 21% strand | B0F481 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.73 | 0.79 | 54 | empty |
| 2 | 691 | 0.73 | 0.79 | 47 | empty |
| 3 | 815 | 0.71 | 0.77 | 68 | empty |
| 4 | 57 | 0.71 | 0.98 | 21 | PLP |
| 5 | 755 | 0.69 | 0.76 | 64 | empty |
Interfaces
1 interface between chains.
- A–B · 7147 Ų buried · 122 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified, 2 cofactor (engineered, pyridoxal phosphate Schiff base).
Compared structures
- 4A0F · Structure of selenomethionine substituted bifunctional DAPA aminotransferase-dethiobiotin… · the same entry in another collection · chain A against A, TM-score 1.00
- B0F481 · AlphaFold monomer V2.0 prediction for bifunctional dethiobiotin… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 B0F481
- Elsewhere: RCSB PDB 4A0F · PDBe 4A0F · UniProt B0F481
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