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Rat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NADH and 3-keto butyrate
Analyse Rat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NADH and 3-keto… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E3W
- Type
- protein
- Length
- 1,001 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, AAE, SO4
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short chain 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 251 | 44% helix, 18% strand | O70351 |
| B | Short chain 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 247 | 44% helix, 18% strand | O70351 |
| C | Short chain 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 248 | 44% helix, 18% strand | O70351 |
| D | Short chain 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 255 | 45% helix, 17% strand | O70351 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- AAE · Acetoacetic acid · ligand · chains D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, C, B, 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 | 1029 | 0.86 | 0.87 | 57 | TRS |
| 2 | 397 | 0.75 | 0.85 | 53 | NAD, AAE |
| 3 | 428 | 0.70 | 0.81 | 46 | NAD |
| 4 | 329 | 0.70 | 0.83 | 43 | NAD |
| 5 | 379 | 0.69 | 0.81 | 44 | NAD |
Interfaces
6 interfaces between chains.
- A–B · 1916 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1907 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1620 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1594 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 225 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1E3W · Rat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NADH and 3-keto butyrate · the same entry in another collection · chain D against D, 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 B against A, TM-score 1.00
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 1E3W · PDBe 1E3W · UniProt O70351
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