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Crystal structure of 7,8-diaminopelargonic acid synthase (bioa) from mycobacterium tuberculosis, pre-reaction complex with a 3,6- dihydropyrid-2-one heterocycle inhibitor
Analyse Crystal structure of 7,8-diaminopelargonic acid synthase (bioa) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TFT
- Type
- protein
- Length
- 846 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
- P0A4X6
- Ligands
- PLP
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 422 | 42% helix, 20% strand | P0A4X6 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 424 | 41% helix, 20% strand | P0A4X6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.76 | 0.82 | 76 | PLP |
| 2 | 444 | 0.72 | 0.82 | 65 | PLP, DMS |
| 3 | 218 | 0.67 | 0.84 | 26 | empty |
| 4 | 65 | 0.34 | 0.77 | 19 | empty |
| 5 | 59 | 0.31 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 4824 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3TFT · 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
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 P0A4X6
- Elsewhere: RCSB PDB 3TFT · PDBe 3TFT · UniProt P0A4X6
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