MolNFT v1 · #124491 · protein
Crystal structure of 7,8-diaminopelargonic acid synthase (bioa) from mycobacterium tuberculosis, complexed with an inhibitor optimized from hts lead: 1-[4-[4-(3-CHLOROPHENYL)CARBONYLPIPERIDIN-1- YL]PHENYL]ETHANONE
5KGT · 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, 6SQ), 5 pockets (best…
- PDB
- 5KGT
- Type
- protein
- Length
- 858 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
- P0A4X7
- Ligands
- PLP, 6SQ
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 429 | 41% helix, 20% strand | P0A4X7 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 429 | 40% helix, 19% strand | P0A4X7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 6SQ · 1-[4-[4-(3-chlorophenyl)carbonylpiperidin-1-yl]phenyl]ethanone · ligand · 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 | 596 | 0.76 | 0.83 | 77 | 6SQ, PLP |
| 2 | 643 | 0.76 | 0.81 | 80 | PLP |
| 3 | 186 | 0.67 | 0.86 | 28 | empty |
| 4 | 81 | 0.37 | 0.76 | 21 | empty |
| 5 | 63 | 0.32 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4750 Ų buried · 59 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5KGT · 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
- P0A4X7 · 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 P0A4X7
- Elsewhere: RCSB PDB 5KGT · PDBe 5KGT · UniProt P0A4X7
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