MolNFT v1 · #109290 · protein
Crystal structure of 7,8-diaminopelargonic acid synthase (bioa) from mycobacterium tuberculosis, complexed with a fragment hit
4WYA · 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, 3VQ), 14 pockets (best…
- PDB
- 4WYA
- Type
- protein
- Length
- 1,675 residues
- Chains
- 4
- 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
- P9WQ81
- Ligands
- PLP, 3VQ
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 420 | 38% helix, 19% strand | P9WQ81 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 422 | 40% helix, 19% strand | P9WQ81 |
| C | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 419 | 39% helix, 19% strand | P9WQ81 |
| D | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 414 | 39% helix, 21% strand | P9WQ81 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- 3VQ · 5-(pyridin-2-yl)thiophene-2-carboxamide · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.79 | 0.82 | 90 | PLP |
| 2 | 588 | 0.77 | 0.83 | 70 | PLP, 3VQ |
| 3 | 860 | 0.76 | 0.79 | 96 | PLP, 3VQ |
| 4 | 571 | 0.74 | 0.82 | 80 | PLP |
| 5 | 511 | 0.70 | 0.80 | 56 | empty |
Interfaces
4 interfaces between chains.
- A–B · 4460 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 4406 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 236 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 126 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4WYA · Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WQ81 · AlphaFold monomer V2.0 prediction for adenosylmethionine-8-amino-7-oxononanoate… · a predicted model of the same protein · chain D 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 P9WQ81
- Elsewhere: RCSB PDB 4WYA · PDBe 4WYA · UniProt P9WQ81
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