MolNFT v1 · #49434 · protein
Crystal structure of the complex between the mycobacterium beta- ketoacyl-acyl carrier protein synthase III (fabh) and 11- [(DECYLOXYCARBONYL)DITHIO]-undecanoic acid
2QNX · 3-oxoacyl-[acyl-carrier-protein] synthase 3: “Crystal structure of the complex between the mycobacterium beta- ketoacyl-acyl carrier protein synthase III…”. X-ray diffraction, 2 ligands (UDT, MDX), 6 pockets (best druggability…
- PDB
- 2QNX
- Type
- protein
- Length
- 666 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
- UDT, MDX
- Pockets
- 6 · best druggability 0.77
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 | 334 | 39% helix, 25% strand | P0A574 |
| B | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.41) | protein | 332 | 36% helix, 24% strand | P0A574 |
Ligands and binding sites
- UDT · O-decyl hydrogen thiocarbonate · ligand · 2 copies · chains A, B
- MDX · 11-mercaptoundecanoic acid · ligand · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.77 | 0.99 | 25 | empty |
| 2 | 210 | 0.75 | 0.90 | 42 | UDT, MDX |
| 3 | 219 | 0.73 | 0.88 | 42 | UDT, MDX |
| 4 | 230 | 0.64 | 0.83 | 56 | empty |
| 5 | 165 | 0.43 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 3108 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2QNX · Crystal structure of the complex between the mycobacterium beta-ketoacyl-acyl carrier… · 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 2QNX · PDBe 2QNX · UniProt P0A574
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