Research workbench
Arabidopsis thaliana mitochondrial beta-ketoacyl acp synthase hexanoic acid complex
Analyse Arabidopsis thaliana mitochondrial beta-ketoacyl acp synthase hexanoic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IX4
- Type
- protein
- Length
- 862 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase
- EC
- 2.3.1.41
- UniProt
- Q8L3X9
- Ligands
- 6NA, K
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxoacyl-[acyl-carrier-protein] synthase (EC 2.3.1.41) | protein | 431 | 40% helix, 21% strand | Q8L3X9 |
Ligands and binding sites
- 6NA · Hexanoic acid · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.75 | 0.88 | 46 | 6NA |
| 2 | 258 | 0.72 | 0.86 | 39 | empty |
| 3 | 155 | 0.48 | 0.77 | 34 | empty |
| 4 | 66 | 0.41 | 0.80 | 14 | empty |
| 5 | 138 | 0.41 | 0.74 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 3504 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2IX4 · Arabidopsis thaliana mitochondrial beta-ketoacyl ACP synthase hexanoic acid complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q8L3X9 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase… · 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 Q8L3X9
- Elsewhere: RCSB PDB 2IX4 · PDBe 2IX4 · UniProt Q8L3X9
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