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Crystal structure of bacillus subtilis beta-ketoacyl-acp synthase II (fabf) in a 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
- 4LS8
- Type
- protein
- Length
- 831 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
- 1XG, NA, CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% 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 | 416 | 38% helix, 22% strand | O34340 |
| B | 3-oxoacyl-[acyl-carrier-protein] synthase 2 (EC 2.3.1.179) | protein | 415 | 39% helix, 22% strand | O34340 |
Ligands and binding sites
- 1XG · (3R,7E,10E)-3-hydroxy-4-oxododeca-7,10-dienamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.76 | 0.87 | 59 | 1XG |
| 2 | 234 | 0.72 | 0.87 | 35 | 1XG |
| 3 | 263 | 0.63 | 0.81 | 50 | EDO |
| 4 | 58 | 0.31 | 0.76 | 14 | empty |
| 5 | 61 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3187 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4LS8 · Crystal structure of Bacillus subtilis beta-ketoacyl-ACP synthase II (FabF) in a covalent… · 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 B against A, TM-score 0.99
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 4LS8 · PDBe 4LS8 · UniProt O34340
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