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Crystal structure of 7,8-diaminopelargonic acid synthase (bioa) from mycobacterium tuberculosis, complexed with a mechanism-based 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
- 5TE2
- 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
- P0A4X7
- Ligands
- 7B9
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 428 | 41% helix, 20% strand | P0A4X7 |
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 428 | 42% helix, 20% strand | P0A4X7 |
Ligands and binding sites
- 7B9 · [5-hydroxy-4-({[6-(3-hydroxypropyl)-4-oxo-1,4-dihydropyridin-3-yl]amino}methyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate · ligand · 2 copies · chains B, A
- PEG · Di(hydroxyethyl)ether · additive · chains B
- EDO · 1,2-ethanediol · additive · chains B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.77 | 0.84 | 72 | 7B9, EDO |
| 2 | 672 | 0.75 | 0.81 | 83 | 7B9 |
| 3 | 218 | 0.66 | 0.84 | 29 | empty |
| 4 | 73 | 0.35 | 0.76 | 22 | empty |
| 5 | 62 | 0.34 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- B–A · 4835 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 5TE2 · Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium… · the same entry in another collection · chain B against B, 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 5TE2 · PDBe 5TE2 · UniProt P0A4X7
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