Research workbench
Crystal structure of (S)-3-hydroxybutyryl-coenzymea dehydrogenase from clostridium acetobutylicum complexed with NAD+
Analyse Crystal structure of (S)-3-hydroxybutyryl-coenzymea dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AA8
- Type
- protein
- Length
- 1,679 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxybutyryl-CoA dehydrogenase
- EC
- 1.1.1.157
- UniProt
- P52041
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) | protein | 280 | 52% helix, 15% strand | P52041 |
| B | 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) | protein | 281 | 52% helix, 15% strand | P52041 |
| C, D, F | 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) | protein | 279 | 53% helix, 15% strand | P52041 |
| E | 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) | protein | 281 | 52% helix, 15% strand | P52041 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.84 | 0.94 | 36 | empty |
| 2 | 296 | 0.83 | 0.94 | 36 | empty |
| 3 | 931 | 0.81 | 0.83 | 98 | empty |
| 4 | 52 | 0.71 | 0.99 | 18 | empty |
| 5 | 546 | 0.67 | 0.77 | 55 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1807 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1797 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1788 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 624 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 618 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6AA8 · Crystal structure of (S)-3-hydroxybutyryl-coenzymeA dehydrogenase from Clostridium… · the same entry in another collection · chain F against F, TM-score 1.00
- P52041 · AlphaFold monomer V2.0 prediction for 3-hydroxybutyryl-CoA dehydrogenase (P52041) · a predicted model of the same protein · chain C 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 P52041
- Elsewhere: RCSB PDB 6AA8 · PDBe 6AA8 · UniProt P52041
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