Research workbench
L-3-hydroxyacyl-CoA dehydrogenase complexed with NADH
Analyse L-3-hydroxyacyl-CoA dehydrogenase complexed with NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F17
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens
- Molecule
- L-3-hydroxyacyl-CoA dehydrogenase
- EC
- 1.1.1.35
- UniProt
- Q16836
- Ligands
- NAI
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 293 | 51% helix, 14% strand | Q16836 |
| B | L-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 291 | 52% helix, 15% strand | Q16836 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.71 | 0.81 | 45 | NAI |
| 2 | 451 | 0.70 | 0.81 | 44 | NAI |
| 3 | 108 | 0.39 | 0.75 | 25 | empty |
| 4 | 96 | 0.38 | 0.76 | 19 | empty |
| 5 | 78 | 0.35 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1658 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1F17 · L-3-hydroxyacyl-CoA dehydrogenase complexed with NADH · the same entry in another collection · chain A against A, TM-score 1.00
- Q16836 · AlphaFold monomer V2.0 prediction for hydroxyacyl-coenzyme a dehydrogenase, mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q16836
- Elsewhere: RCSB PDB 1F17 · PDBe 1F17 · UniProt Q16836
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