MolNFT v1 · #109296 · protein
Crystal structure of 7,8-diaminopelargonic acid synthase (bioa) from mycobacterium tuberculosis complexed with a fragment hit
4WYG · Adenosylmethionine-8-amino-7-oxononanoate aminotransferase: “Crystal structure of 7,8-diaminopelargonic acid synthase (bioa) from mycobacterium tuberculosis complexed…”. X-ray diffraction, 2 ligands (3W1, PLP), 6 pockets (best…
- PDB
- 4WYG
- 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
- P9WQ81
- Ligands
- 3W1, PLP
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 429 | 41% helix, 20% strand | P9WQ81 |
Ligands and binding sites
- 3W1 · 1-{4-[(4-chloro-1H-pyrazol-1-yl)methyl]phenyl}methanamine · ligand · 3 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.76 | 0.84 | 74 | PLP, EPE, 3W1, EDO |
| 2 | 616 | 0.76 | 0.82 | 86 | PLP, EPE, 3W1 |
| 3 | 249 | 0.66 | 0.82 | 28 | empty |
| 4 | 62 | 0.33 | 0.77 | 19 | empty |
| 5 | 62 | 0.31 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4930 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4WYG · 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
- P9WQ81 · AlphaFold monomer V2.0 prediction for adenosylmethionine-8-amino-7-oxononanoate… · a predicted model of the same protein · chain B 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 4WYG · PDBe 4WYG · UniProt P9WQ81
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