MolNFT v1 · #40582 · protein
Human mitochondrial beta-ketoacyl acp synthase complexed with hexanoic acid
2IWZ · 3-oxoacyl-[acyl-carrier-protein] synthase: “Human mitochondrial beta-ketoacyl acp synthase complexed with hexanoic acid”. X-ray diffraction, 2 ligands (6NA, NH4), 9 pockets (best druggability 0.74). MolNFT v1 #40582 on GenesisL1: 3D…
- PDB
- 2IWZ
- Type
- protein
- Length
- 852 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
- Q9NWU1
- Ligands
- 6NA, NH4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxoacyl-[acyl-carrier-protein] synthase (EC 2.3.1.41) | protein | 426 | 38% helix, 23% strand | Q9NWU1 |
Ligands and binding sites
- 6NA · Hexanoic acid · ligand · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · 2 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 | 228 | 0.74 | 0.88 | 42 | 6NA |
| 2 | 220 | 0.73 | 0.88 | 35 | empty |
| 3 | 79 | 0.72 | 0.96 | 22 | empty |
| 4 | 146 | 0.45 | 0.77 | 24 | empty |
| 5 | 124 | 0.42 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3799 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2IWZ · Human mitochondrial beta-ketoacyl ACP synthase complexed with hexanoic acid · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NWU1 · 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 Q9NWU1
- Elsewhere: RCSB PDB 2IWZ · PDBe 2IWZ · UniProt Q9NWU1
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