MolNFT v1 · #26054 · protein
Fatty acid beta-oxidation multienzyme complex from pseudomonas fragi, form II (NATIVE4)
1WDL · Fatty oxidation complex alpha subunit: “Fatty acid beta-oxidation multienzyme complex from pseudomonas fragi, form II (NATIVE4)”. X-ray diffraction, 3 ligands (N8E, ACO, NAD), 20 pockets (best druggability 0.82). MolNFT v1 #26054 on…
- PDB
- 1WDL
- Type
- protein
- Length
- 2,201 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty oxidation complex alpha subunit; 3-ketoacyl-CoA thiolase
- EC
- 4.2.1.17, 5.3.3.8, 1.1.1.35, 5.1.2.3, 2.3.1.16
- UniProt
- P28793, P28790
- Ligands
- N8E, ACO, NAD
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fatty oxidation complex alpha subunit (EC 4.2.1.17, 5.3.3.8, 1.1.1.35, 5.1.2.3) | protein | 715 | 54% helix, 13% strand | P28793 |
| B | Fatty oxidation complex alpha subunit (EC 4.2.1.17, 5.3.3.8, 1.1.1.35, 5.1.2.3) | protein | 706 | 54% helix, 12% strand | P28793 |
| C, D | 3-ketoacyl-CoA thiolase (EC 2.3.1.16) | protein | 390 | 39% helix, 22% strand | P28790 |
Ligands and binding sites
- N8E · 3,6,9,12,15-pentaoxatricosan-1-ol · ligand · 3 copies · chains A, B
- ACO · Acetyl coenzyme *A · ligand · 2 copies · chains C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.82 | 0.84 | 79 | empty |
| 2 | 1056 | 0.80 | 0.81 | 84 | N8E |
| 3 | 669 | 0.77 | 0.82 | 77 | NAD |
| 4 | 741 | 0.76 | 0.81 | 51 | empty |
| 5 | 218 | 0.72 | 0.88 | 38 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2710 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 950 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 934 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 823 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 552 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1WDL · fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form II (native4) · the same entry in another collection · chain D against D, TM-score 1.00
- P28790 · AlphaFold monomer V2.0 prediction for 3-ketoacyl-CoA thiolase (P28790) · a predicted model of the same protein · chain D against A, TM-score 1.00
- P28793 · AlphaFold monomer V2.0 prediction for fatty acid oxidation complex subunit alpha (P28793) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P28793
- Every structure of UniProt P28790
- Elsewhere: RCSB PDB 1WDL · PDBe 1WDL · UniProt P28793 · UniProt P28790
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