MolNFT v1 · #91400 · protein
Studies on dcr shed new light on peroxisomal beta-oxidation: crystal structure of the ternary complex of pdcr
4FC6 · Peroxisomal 2,4-dienoyl-CoA reductase: “Studies on dcr shed new light on peroxisomal beta-oxidation: crystal structure of the ternary complex of pdcr”. X-ray diffraction, 2 ligands (NAP, HXC), 9 pockets (best druggability 0.83).…
- PDB
- 4FC6
- Type
- protein
- Length
- 1,098 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal 2,4-dienoyl-CoA reductase
- EC
- 1.3.1.34
- UniProt
- Q9NUI1
- Ligands
- NAP, HXC
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) | protein | 274 | 49% helix, 15% strand | Q9NUI1 |
| B | Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) | protein | 276 | 48% helix, 15% strand | Q9NUI1 |
| C | Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) | protein | 276 | 48% helix, 15% strand | Q9NUI1 |
| D | Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) | protein | 272 | 50% helix, 15% strand | Q9NUI1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- HXC · Hexanoyl-coenzyme A · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.83 | 0.84 | 77 | empty |
| 2 | 679 | 0.83 | 0.87 | 59 | NAP |
| 3 | 670 | 0.82 | 0.87 | 62 | NAP |
| 4 | 689 | 0.82 | 0.86 | 65 | NAP |
| 5 | 659 | 0.81 | 0.86 | 60 | NAP |
Interfaces
6 interfaces between chains.
- A–C · 1849 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1810 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1661 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1636 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 300 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4FC6 · Studies on DCR shed new light on peroxisomal beta-oxidation: Crystal structure of the… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NUI1 · AlphaFold monomer V2.0 prediction for peroxisomal 2,4-dienoyl-CoA reductase… · 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 Q9NUI1
- Elsewhere: RCSB PDB 4FC6 · PDBe 4FC6 · UniProt Q9NUI1
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