MolNFT v1 · #5508 · protein
Beta-ketoacyl [acyl carrier protein] synthase I in complex with dodecanoic acid to 1.85 resolution
1EK4: “Beta-ketoacyl [acyl carrier protein] synthase I in complex with dodecanoic acid to 1.85 resolution”. X-ray diffraction, 1 ligand (DAO), 12 pockets (best druggability 0.76). MolNFT v1 #5508 on GenesisL1: 3D structure, binding sites…
- PDB
- 1EK4
- Type
- protein
- Length
- 1,624 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
- DAO
- Pockets
- 12 · best druggability 0.76
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 | 406 | 38% helix, 22% strand | P0A953 |
Ligands and binding sites
- DAO · Lauric acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.76 | 0.90 | 45 | DAO |
| 2 | 77 | 0.75 | 0.98 | 20 | DAO |
| 3 | 86 | 0.75 | 0.97 | 22 | DAO |
| 4 | 225 | 0.74 | 0.89 | 46 | DAO |
| 5 | 153 | 0.62 | 0.85 | 34 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2920 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2919 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 222 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 121 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 115 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1EK4 · Beta-ketoacyl [acyl carrier protein] synthase I in complex with dodecanoic acid to 1.85… · the same entry in another collection · chain A against A, 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 D 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 1EK4 · PDBe 1EK4 · UniProt P0A953
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