MolNFT v1 · #108353 · protein
Crystal structure of 7,8-diaminopelargonic acid synthase (bioa) from mycobacterium tuberculosis, complexed with 1-(4-(4-(3-chlorobenzoyl) piperazin-1-YL)PHENYL)ETHANONE
4W1X · 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, 3G9), 5 pockets (best…
- PDB
- 4W1X
- 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
- P9WQ80
- Ligands
- PLP, 3G9
- 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 | P9WQ80 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 429 | 40% helix, 19% strand | P9WQ80 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 3G9 · 1-{4-[4-(3-chlorobenzoyl)piperazin-1-yl]phenyl}ethanone · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.76 | 0.81 | 85 | PLP, 3G9 |
| 2 | 82 | 0.73 | 0.96 | 33 | PLP |
| 3 | 537 | 0.71 | 0.80 | 61 | 3G9 |
| 4 | 190 | 0.67 | 0.86 | 28 | empty |
| 5 | 63 | 0.32 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4877 Ų buried · 63 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4W1X · 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
- P9WQ80 · 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 P9WQ80
- Elsewhere: RCSB PDB 4W1X · PDBe 4W1X · UniProt P9WQ80
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