Research workbench
The structure of beta-ketoacyl-[acyl carrier protein] synthase I in complex with cerulenin, implications for drug design
Analyse The structure of beta-ketoacyl-[acyl carrier protein] synthase I in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FJ8
- Type
- protein
- Length
- 1,612 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-ketoacyl-[acyl carrier protein] synthase I
- EC
- 2.3.1.41
- UniProt
- P0A953
- Ligands
- CER
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-ketoacyl-[acyl carrier protein] synthase I (EC 2.3.1.41) | protein | 403 | 38% helix, 22% strand | P0A953 |
Ligands and binding sites
- CER · (2S, 3R)-3-hydroxy-4-oxo-7,10-trans,trans-dodecadienamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.75 | 0.88 | 50 | CER |
| 2 | 272 | 0.75 | 0.88 | 51 | CER |
| 3 | 272 | 0.75 | 0.88 | 50 | CER |
| 4 | 253 | 0.74 | 0.88 | 50 | CER |
| 5 | 176 | 0.42 | 0.73 | 26 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3017 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 3000 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 118 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1FJ8 · The structure of beta-ketoacyl-[acyl carrier protein] synthase I in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P0A953 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 1… · a predicted model of the same protein · chain C 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 P0A953
- Elsewhere: RCSB PDB 1FJ8 · PDBe 1FJ8 · UniProt P0A953
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