MolNFT v1 · #85054 · protein
Structure of bifunctional dapa aminotransferase-dtb synthetase from arabidopsis thaliana in its apo form.
4A0G · Adenosylmethionine-8-amino-7-oxononanoate aminotransferase: “Structure of bifunctional dapa aminotransferase-dtb synthetase from arabidopsis thaliana in its apo form.”. X-ray diffraction, 3 ligands (PLP, MG, SO4), 20 pockets (best…
- PDB
- 4A0G
- Type
- protein
- Length
- 2,915 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
- UniProt
- B0F481
- Ligands
- PLP, MG, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | protein | 769 | 38% helix, 22% strand | B0F481 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | protein | 756 | 39% helix, 22% strand | B0F481 |
| C | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | protein | 681 | 38% helix, 23% strand | B0F481 |
| D | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | protein | 709 | 39% helix, 23% strand | B0F481 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.78 | 0.80 | 100 | empty |
| 2 | 1022 | 0.77 | 0.79 | 93 | empty |
| 3 | 714 | 0.73 | 0.79 | 59 | empty |
| 4 | 65 | 0.73 | 0.98 | 26 | PLP |
| 5 | 589 | 0.72 | 0.80 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–B · 7442 Ų buried · 135 hydrogen bonds · protein-protein
- C–D · 5544 Ų buried · 88 hydrogen bonds · protein-protein
- A–C · 341 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 123 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 97 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4A0G · Structure of bifunctional DAPA aminotransferase-DTB synthetase from Arabidopsis thaliana… · the same entry in another collection · chain D against D, TM-score 1.00
- B0F481 · AlphaFold monomer V2.0 prediction for bifunctional dethiobiotin… · a predicted model of the same protein · chain C 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 4A0G · PDBe 4A0G · UniProt B0F481
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