Research workbench
Three-dimensional structure of butyryl-CoA dehydrogenase from megasphaera elsdenii
Analyse Three-dimensional structure of butyryl-CoA dehydrogenase from megasphaera… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BUC
- Type
- protein
- Length
- 766 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Butyryl-CoA dehydrogenase
- EC
- 1.3.99.2
- UniProt
- Q06319
- Ligands
- CAA, FAD
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Butyryl-CoA dehydrogenase (EC 1.3.99.2) | protein | 383 | 58% helix, 16% strand | Q06319 |
Ligands and binding sites
- CAA · Acetoacetyl-coenzyme A · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.70 | 0.82 | 41 | CAA, FAD |
| 2 | 347 | 0.70 | 0.82 | 42 | CAA, FAD |
| 3 | 236 | 0.57 | 0.79 | 19 | empty |
| 4 | 146 | 0.45 | 0.76 | 31 | empty |
| 5 | 131 | 0.40 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1932 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1BUC · Three-dimensional structure of butyryl-CoA dehydrogenase from megasphaera elsdenii · the same entry in another collection · chain A against A, TM-score 1.00
- Q06319 · AlphaFold monomer V2.0 prediction for acyl-CoA dehydrogenase, short- chain specific… · a predicted model of the same protein · chain A 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 Q06319
- Elsewhere: RCSB PDB 1BUC · PDBe 1BUC · UniProt Q06319
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