MolNFT v1 · #31285 · protein
Structure-activity relationships at the 5-posiiton of thiolactomycin: an intact 5(R)-isoprene unit is required for activity against the condensing enzymes from mycobacterium tuberculosis and escherichia COLI
2AQ7 · 3-oxoacyl-[acyl-carrier-protein] synthase I: “Structure-activity relationships at the 5-posiiton of thiolactomycin: an intact 5(R)-isoprene unit is…”. X-ray diffraction, 1 ligand (TL5), 11 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 2AQ7
- 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
- TL5
- Pockets
- 11 · best druggability 0.75
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, 23% strand | P0A953 |
Ligands and binding sites
- TL5 · (5R)-4-hydroxy-3,5-dimethyl-5-[(1E,3E)-2-methylpenta-1,3-dienyl]thiophen-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 | 212 | 0.75 | 0.90 | 51 | empty |
| 2 | 188 | 0.71 | 0.88 | 38 | TL5 |
| 3 | 190 | 0.70 | 0.87 | 36 | TL5 |
| 4 | 201 | 0.69 | 0.86 | 37 | TL5 |
| 5 | 104 | 0.39 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3050 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 3037 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 104 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2AQ7 · Structure-activity relationships at the 5-posiiton of thiolactomycin: an intact… · the same entry in another collection · chain C against C, 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 2AQ7 · PDBe 2AQ7 · UniProt P0A953
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