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Crystal structure of 7,8-diaminopelargonic acid synthase (bioa) from mycobacterium tuberculosis, complexed with 7-(diethylamino)-3- (thiophene-2-carbonyl)-2H-chromen-2-one
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
- 4W1W
- Type
- protein
- Length
- 857 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, 3G8, CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% 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 | 40% helix, 20% strand | P9WQ80 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 428 | 40% helix, 19% strand | P9WQ80 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 3G8 · 7-(diethylamino)-3-(thiophen-2-ylcarbonyl)-2H-chromen-2-one · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.77 | 0.82 | 93 | PLP, 3G8 |
| 2 | 83 | 0.73 | 0.96 | 33 | PLP |
| 3 | 584 | 0.71 | 0.79 | 66 | 3G8 |
| 4 | 181 | 0.63 | 0.84 | 28 | empty |
| 5 | 71 | 0.35 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4946 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4W1W · 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 4W1W · PDBe 4W1W · UniProt P9WQ80
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