Research workbench
Structure of bifunctional dapa aminotransferase-dtb synthetase from arabidopsis thaliana bound to dethiobiotin (dtb).
Analyse Structure of bifunctional dapa aminotransferase-dtb synthetase from arabidopsis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A0R
- Type
- protein
- Length
- 1,503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
- EC
- 6.3.3.3, 2.6.1.62
- UniProt
- B0F481
- Ligands
- PLP, DTB
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 6.3.3.3, 2.6.1.62) | protein | 755 | 38% helix, 22% strand | B0F481 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 6.3.3.3, 2.6.1.62) | protein | 748 | 38% helix, 23% strand | B0F481 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- DTB · 6-(5-methyl-2-oxo-imidazolidin-4-yl)-hexanoic acid · ligand · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.71 | 0.80 | 61 | PLP |
| 2 | 705 | 0.71 | 0.78 | 48 | empty |
| 3 | 679 | 0.71 | 0.78 | 46 | empty |
| 4 | 496 | 0.70 | 0.80 | 59 | PLP |
| 5 | 579 | 0.65 | 0.76 | 57 | empty |
Interfaces
1 interface between chains.
- A–B · 7399 Ų buried · 129 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4A0R · Structure of bifunctional DAPA aminotransferase-DTB synthetase from Arabidopsis thaliana… · 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 A 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 4A0R · PDBe 4A0R · UniProt B0F481
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