MolNFT v2 · #14383 · protein
Crystal Structure of the S137C Mutant of L-3-HYDROXYACYL-COA Dehydrogenase in Complex with NAD and Acetoacetyl-COA
1M76: “Crystal Structure of the S137C Mutant of L-3-HYDROXYACYL-COA Dehydrogenase in Complex with NAD and…”. X-ray diffraction at 2.15, 2 ligands (CAA, NAD), 4 pockets (best druggability 0.74). MolNFT v2 #14383 on GenesisL1: 3D structure…
- PDB
- 1M76
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Homo sapiens
- Molecule
- 3-hydroxyacyl-CoA dehydrogenase
- EC
- 1.1.1.35
- UniProt
- Q16836
- Ligands
- CAA, NAD
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.15 · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 291 | 51% helix, 14% strand | Q16836 |
Ligands and binding sites
- CAA · Acetoacetyl-coenzyme A · ligand · 2 copies · chains A, B
- 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.74 | 0.80 | 71 | CAA, NAD |
| 2 | 656 | 0.74 | 0.80 | 72 | CAA, NAD |
| 3 | 111 | 0.40 | 0.76 | 20 | empty |
| 4 | 52 | 0.31 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1648 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1M76 · Crystal structure of the S137C mutant of L-3-hydroxyacyl-CoA dehydrogenase in complex… · 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 0.93
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 1M76 · PDBe 1M76 · UniProt Q16836
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