MolNFT v1 · #49435 · protein
Crystal structure of the complex between the A246F mutant of mycobacterium beta-ketoacyl-acyl carrier protein synthase III (fabh) and ss-(2-hydroxyethyl) O-decyl ester CARBONO(DITHIOPEROXOIC) acid
2QNY · 3-oxoacyl-[acyl-carrier-protein] synthase 3: “Crystal structure of the complex between the A246F mutant of mycobacterium beta-ketoacyl-acyl carrier protein…”. X-ray diffraction, 1 ligand (DFD), 9 pockets (best druggability 0.78).…
- PDB
- 2QNY
- Type
- protein
- Length
- 659 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 3
- EC
- 2.3.1.41
- UniProt
- P0A574
- Ligands
- DFD
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.41) | protein | 330 | 38% helix, 25% strand | P0A574 |
| B | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.41) | protein | 329 | 39% helix, 24% strand | P0A574 |
Ligands and binding sites
- DFD · Decyl formate · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.78 | 0.99 | 22 | empty |
| 2 | 87 | 0.77 | 0.98 | 26 | DFD |
| 3 | 77 | 0.75 | 0.98 | 26 | DFD |
| 4 | 150 | 0.61 | 0.85 | 38 | empty |
| 5 | 86 | 0.42 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3225 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (additive adduct, covalent ligand).
Compared structures
- 2QNY · Crystal structure of the complex between the A246F mutant of mycobacterium… · the same entry in another collection · 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 P0A574
- Elsewhere: RCSB PDB 2QNY · PDBe 2QNY · UniProt P0A574
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