Research workbench
Biochemical characterization and structure determination of human heart short chain L-3-hydroxyacyl CoA dehydrogenase provide insight into catalytic mechanism
Analyse Biochemical characterization and structure determination of human heart short… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HDH
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-3-hydroxyacyl CoA dehydrogenase
- EC
- 1.1.1.35
- UniProt
- Q16836
- Ligands
- NAD
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-3-hydroxyacyl CoA dehydrogenase (EC 1.1.1.35) | protein | 293 | 50% helix, 14% strand | Q16836 |
| B | L-3-hydroxyacyl CoA dehydrogenase (EC 1.1.1.35) | protein | 291 | 52% helix, 14% strand | Q16836 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.70 | 0.80 | 44 | NAD |
| 2 | 439 | 0.69 | 0.81 | 44 | NAD |
| 3 | 98 | 0.37 | 0.75 | 20 | empty |
| 4 | 69 | 0.35 | 0.77 | 19 | empty |
| 5 | 95 | 0.34 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1654 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2HDH · Biochemical characterization and structure determination of human heart short chain… · 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 B 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 2HDH · PDBe 2HDH · UniProt Q16836
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