MolNFT v1 · #31289 · protein
Structure-activity relationships at the 5-position of thiolactomycin: an intact 5(R)-isoprene unit is required for activity against the condensing enzymes from mycobacterium tuberculosis and escherchia COLI
2AQB · 3-oxoacyl-[acyl-carrier-protein] synthase I: “Structure-activity relationships at the 5-position of thiolactomycin: an intact 5(R)-isoprene unit is…”. X-ray diffraction, 1 ligand (TL6), 11 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 2AQB
- Type
- protein
- Length
- 1,613 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase I
- EC
- 2.3.1.41
- UniProt
- P0A953
- Ligands
- TL6
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier-protein] synthase I (EC 2.3.1.41) | protein | 404 | 37% helix, 22% strand | P0A953 |
| B, C, D | 3-oxoacyl-[acyl-carrier-protein] synthase I (EC 2.3.1.41) | protein | 403 | 38% helix, 22% strand | P0A953 |
Ligands and binding sites
- TL6 · (5R)-5-[(1E)-buta-1,3-dienyl]-4-hydroxy-3,5-dimethylthiophen-2(5H)-one · ligand · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.73 | 0.89 | 50 | TL6 |
| 2 | 186 | 0.72 | 0.89 | 49 | empty |
| 3 | 187 | 0.67 | 0.86 | 38 | TL6 |
| 4 | 170 | 0.66 | 0.86 | 34 | TL6 |
| 5 | 106 | 0.39 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3059 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3030 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 103 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2AQB · Structure-activity relationships at the 5-position of thiolactomycin: an intact… · the same entry in another collection · chain D against D, TM-score 1.00
- P0A953 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 1… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P0A953
- Elsewhere: RCSB PDB 2AQB · PDBe 2AQB · UniProt P0A953
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.