MolNFT v1 · #4962 · protein
Rat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NADH
1E3S · Short chain 3-hydroxyacyl-CoA dehydrogenase: “Rat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NADH”. X-ray diffraction, 1 ligand (NAD), 9 pockets (best druggability 0.84). MolNFT v1 #4962 on GenesisL1: 3D structure…
- PDB
- 1E3S
- Type
- protein
- Length
- 964 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain 3-hydroxyacyl-CoA dehydrogenase
- EC
- 1.1.1.35
- UniProt
- O70351
- Ligands
- NAD
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Short chain 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 241 | 42% helix, 18% strand | O70351 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.84 | 0.85 | 67 | empty |
| 2 | 335 | 0.61 | 0.78 | 40 | NAD |
| 3 | 320 | 0.61 | 0.78 | 39 | NAD |
| 4 | 363 | 0.61 | 0.77 | 37 | NAD |
| 5 | 306 | 0.59 | 0.77 | 37 | NAD |
Interfaces
6 interfaces between chains.
- C–D · 1935 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1834 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1665 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1630 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 178 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1E3S · Rat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NADH · the same entry in another collection · chain A against A, TM-score 1.00
- O70351 · AlphaFold monomer V2.0 prediction for 3-hydroxyacyl-CoA dehydrogenase type-2 (O70351) · 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 O70351
- Elsewhere: RCSB PDB 1E3S · PDBe 1E3S · UniProt O70351
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