Research workbench
Studies on dcr shed new light on peroxisomal beta-oxidation: crystal structure of the ternary complex of pdcr
Analyse Studies on dcr shed new light on peroxisomal beta-oxidation: crystal structure… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FC7
- 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, COA
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 50% 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 | 50% helix, 15% strand | Q9NUI1 |
| B | Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) | protein | 276 | 50% helix, 15% strand | Q9NUI1 |
| C | Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) | protein | 276 | 49% helix, 15% strand | Q9NUI1 |
| D | Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) | protein | 272 | 49% helix, 15% strand | Q9NUI1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- COA · 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 | 1159 | 0.84 | 0.85 | 76 | empty |
| 2 | 676 | 0.83 | 0.87 | 64 | NAP |
| 3 | 701 | 0.82 | 0.86 | 66 | NAP |
| 4 | 707 | 0.82 | 0.86 | 67 | NAP |
| 5 | 654 | 0.82 | 0.86 | 61 | NAP |
Interfaces
6 interfaces between chains.
- B–D · 1817 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1813 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1671 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1635 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 310 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4FC7 · 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 C 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 4FC7 · PDBe 4FC7 · UniProt Q9NUI1
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