MolNFT v1 · #129458 · protein
The electron transferring FLAVOPROTEIN/BUTYRYL-CoA dehydrogenase complex from clostridium difficile
5OL2 · Electron transfer flavoprotein large subunit: “The electron transferring FLAVOPROTEIN/BUTYRYL-CoA dehydrogenase complex from clostridium difficile”. X-ray diffraction, 3 ligands (FAD, COS, CA), 20 pockets (best druggability 0.82).…
- PDB
- 5OL2
- Type
- protein
- Length
- 1,938 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Electron transfer flavoprotein large subunit; Electron transfer flavoprotein small…
- EC
- 1.3.8.1, 1.3.99.-
- UniProt
- A0A031WK27, A0A031WJM1, A0A031WJ47
- Ligands
- FAD, COS, CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Electron transfer flavoprotein large subunit | protein | 331 | 32% helix, 26% strand | A0A031WK27 |
| B, E | Electron transfer flavoprotein small subunit | protein | 260 | 31% helix, 28% strand | A0A031WJM1 |
| C, F | Acyl-CoA dehydrogenase (EC 1.3.8.1, 1.3.99.-) | protein | 378 | 56% helix, 15% strand | A0A031WJ47 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, C, F, B, D, E
- COS · Coenzyme A persulfide · ligand · 2 copies · chains C, F
- CA · Calcium ion · metal · 5 copies · chains A, C, D, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.82 | 0.87 | 58 | FAD |
| 2 | 558 | 0.82 | 0.87 | 57 | FAD |
| 3 | 705 | 0.80 | 0.84 | 73 | FAD |
| 4 | 692 | 0.79 | 0.84 | 75 | FAD |
| 5 | 1126 | 0.74 | 0.77 | 100 | empty |
Interfaces
9 interfaces between chains.
- A–B · 3302 Ų buried · 59 hydrogen bonds · protein-protein
- D–E · 3267 Ų buried · 51 hydrogen bonds · protein-protein
- C–F · 1970 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 840 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 819 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 1 covalent (flavinylation, covalent ligand).
Compared structures
- 5OL2 · The electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium… · the same entry in another collection · 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 A0A031WK27
- Every structure of UniProt A0A031WJM1
- Every structure of UniProt A0A031WJ47
- Elsewhere: RCSB PDB 5OL2 · PDBe 5OL2 · UniProt A0A031WK27 · UniProt A0A031WJM1 · UniProt A0A031WJ47
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