MolNFT v1 · #85055 · protein
Structure of bifunctional dapa aminotransferase-dtb synthetase from arabidopsis thaliana bound to 7-keto 8-amino pelargonic acid (kapa)
4A0H · Adenosylmethionine-8-amino-7-oxononanoate aminotransferase: “Structure of bifunctional dapa aminotransferase-dtb synthetase from arabidopsis thaliana bound to 7-keto…”. X-ray diffraction, 2 ligands (KAP, PLP), 10 pockets (best…
- PDB
- 4A0H
- Type
- protein
- Length
- 1,486 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
- KAP, PLP
- Pockets
- 10 · best druggability 0.75
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 | 748 | 37% helix, 22% strand | B0F481 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | protein | 738 | 37% helix, 21% strand | B0F481 |
Ligands and binding sites
- KAP · 7-keto-8-aminopelargonic acid · ligand · 4 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · 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
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.75 | 0.78 | 139 | PLP, KAP |
| 2 | 723 | 0.72 | 0.78 | 44 | empty |
| 3 | 719 | 0.72 | 0.78 | 45 | empty |
| 4 | 405 | 0.70 | 0.82 | 64 | PLP, KAP |
| 5 | 378 | 0.66 | 0.80 | 57 | KAP, TLA |
Interfaces
1 interface between chains.
- A–B · 7383 Ų buried · 121 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4A0H · 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 4A0H · PDBe 4A0H · UniProt B0F481
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