Research workbench
Bacillus subtilis bioa in complex with amino donor L-lys
Analyse Bacillus subtilis bioa in complex with amino donor L-lys in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WNN
- Type
- protein
- Length
- 836 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
- A0A162RZA9
- Ligands
- LLP, PMP
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 420 | 44% helix, 20% strand | A0A162RZA9 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 416 | 43% helix, 18% strand | A0A162RZA9 |
Ligands and binding sites
- LLP · (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid · ligand · chains A, B
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.84 | 0.85 | 132 | LLP, PMP |
| 2 | 206 | 0.46 | 0.74 | 31 | empty |
| 3 | 80 | 0.33 | 0.74 | 18 | empty |
| 4 | 61 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 4608 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 6WNN · Bacillus subtilis BioA in complex with amino donor L-Lys · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A162RZA9
- Elsewhere: RCSB PDB 6WNN · PDBe 6WNN · UniProt A0A162RZA9
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