Research workbench
Fatty acid beta-oxidation multienzyme complex from pseudomonas fragi, form I (NATIVE3)
Analyse Fatty acid beta-oxidation multienzyme complex from pseudomonas fragi, form I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WDM
- Type
- protein
- Length
- 2,197 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
- ACO, NAD, ZN
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 51% 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 | 707 | 54% helix, 12% 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 | 710 | 54% helix, 12% strand | P28793 |
| C, D | 3-ketoacyl-CoA thiolase (EC 2.3.1.16) | protein | 390 | 40% helix, 22% strand | P28790 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 3 copies · chains A, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.80 | 0.81 | 111 | empty |
| 2 | 675 | 0.75 | 0.81 | 62 | empty |
| 3 | 714 | 0.73 | 0.79 | 93 | empty |
| 4 | 61 | 0.73 | 0.99 | 19 | empty |
| 5 | 338 | 0.72 | 0.84 | 52 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2741 Ų buried · 70 hydrogen bonds · protein-protein
- A–B · 834 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 815 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 771 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 498 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1WDM · fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native3) · 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 0.98
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 1WDM · PDBe 1WDM · UniProt P28793 · UniProt P28790
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