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Crystal structure of bacillus subtilis beta-ketoacyl-acp synthase II (fabf) in a non-covalent complex with cerulenin
Analyse Crystal structure of bacillus subtilis beta-ketoacyl-acp synthase II (fabf) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LS7
- Type
- protein
- Length
- 827 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
- 1X9, K
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% 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 | 414 | 41% helix, 21% strand | O34340 |
Ligands and binding sites
- 1X9 · Cerulenin · ligand · 2 copies · chains A, B
- 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.78 | 0.89 | 56 | 1X9 |
| 2 | 357 | 0.77 | 0.87 | 59 | 1X9 |
| 3 | 176 | 0.58 | 0.82 | 33 | GOL |
| 4 | 66 | 0.47 | 0.84 | 20 | empty |
| 5 | 95 | 0.36 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3102 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4LS7 · Crystal structure of Bacillus subtilis beta-ketoacyl-ACP synthase II (FabF) in a… · 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 4LS7 · PDBe 4LS7 · UniProt O34340
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