Research workbench
Crystal structure of beta-ketoacyl-acp synthase II (fabf) from bacillus subtilis
Analyse Crystal structure of beta-ketoacyl-acp synthase II (fabf) from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LS5
- Type
- protein
- Length
- 825 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 2
- EC
- 2.3.1.179
- UniProt
- O34340
- Ligands
- K
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 (EC 2.3.1.179) | protein | 413 | 40% helix, 22% strand | O34340 |
| B | 3-oxoacyl-[acyl-carrier-protein] synthase 2 (EC 2.3.1.179) | protein | 412 | 40% helix, 21% strand | O34340 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.74 | 0.98 | 21 | empty |
| 2 | 199 | 0.70 | 0.87 | 46 | empty |
| 3 | 156 | 0.60 | 0.83 | 33 | empty |
| 4 | 96 | 0.42 | 0.78 | 18 | empty |
| 5 | 97 | 0.36 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2962 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4LS5 · Crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- O34340 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 2… · 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 O34340
- Elsewhere: RCSB PDB 4LS5 · PDBe 4LS5 · UniProt O34340
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