MolNFT v1 · #109851 · protein
Crystal structure of 7,8-diaminopelargonic acid synthase (bioa) from mycobacterium tuberculosis, complexed with a hts lead compound
4XEW · Adenosylmethionine-8-amino-7-oxononanoate aminotransferase: “Crystal structure of 7,8-diaminopelargonic acid synthase (bioa) from mycobacterium tuberculosis, complexed…”. X-ray diffraction, 2 ligands (PLP, 40N), 6 pockets (best…
- PDB
- 4XEW
- Type
- protein
- Length
- 856 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
- EC
- 2.6.1.62
- UniProt
- P9WQ81
- Ligands
- PLP, 40N
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 428 | 40% helix, 20% strand | P9WQ81 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 40N · 6-(2-fluorophenyl)[1,3]dioxolo[4,5-g]quinolin-8(5H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.76 | 0.82 | 89 | PLP, 40N |
| 2 | 68 | 0.70 | 0.96 | 28 | PLP |
| 3 | 469 | 0.69 | 0.80 | 62 | 40N |
| 4 | 178 | 0.65 | 0.85 | 27 | empty |
| 5 | 61 | 0.34 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 4927 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 4XEW · Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WQ81 · AlphaFold monomer V2.0 prediction for adenosylmethionine-8-amino-7-oxononanoate… · 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 P9WQ81
- Elsewhere: RCSB PDB 4XEW · PDBe 4XEW · UniProt P9WQ81
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.