MolNFT v1 · #66001 · protein
Pig heart short chain L-3-hydroxyacyl CoA dehydrogenase revisited: sequence analysis and crystal structure determination
3HDH · Protein (L-3-hydroxyacyl CoA dehydrogenase): “Pig heart short chain L-3-hydroxyacyl CoA dehydrogenase revisited: sequence analysis and crystal structure…”. X-ray diffraction, 1 ligand (NAD), 15 pockets (best druggability 0.69).…
- PDB
- 3HDH
- Type
- protein
- Length
- 847 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (L-3-hydroxyacyl CoA dehydrogenase)
- EC
- 1.1.1.35
- UniProt
- P00348
- Ligands
- NAD
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (L-3-hydroxyacyl CoA dehydrogenase) (EC 1.1.1.35) | protein | 291 | 50% helix, 14% strand | P00348 |
| C | Protein (L-3-hydroxyacyl CoA dehydrogenase) (EC 1.1.1.35) | protein | 265 | 46% helix, 15% strand | P00348 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.69 | 0.80 | 44 | NAD |
| 2 | 495 | 0.68 | 0.79 | 43 | NAD |
| 3 | 350 | 0.68 | 0.81 | 41 | NAD |
| 4 | 349 | 0.61 | 0.77 | 28 | empty |
| 5 | 176 | 0.57 | 0.81 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1640 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 314 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 85 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3HDH · Pig heart short chain L-3-hydroxyacyl CoA dehydrogenase revisited: sequence analysis and… · the same entry in another collection · chain C against C, TM-score 1.00
- P00348 · 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 P00348
- Elsewhere: RCSB PDB 3HDH · PDBe 3HDH · UniProt P00348
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