Research workbench
3-sulfinopropionyl-coenzyme a (3SP-CoA) desulfinase from advenella mimigardefordensis DPN7T: crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold. native crystal structure
Analyse 3-sulfinopropionyl-coenzyme a (3SP-CoA) desulfinase from advenella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AF7
- Type
- protein
- Length
- 781 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase
- EC
- 3.13.1.4
- UniProt
- K4L7X3
- Ligands
- FAD
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA dehydrogenase (EC 3.13.1.4) | protein | 390 | 54% helix, 17% strand | K4L7X3 |
| B | Acyl-CoA dehydrogenase (EC 3.13.1.4) | protein | 391 | 54% helix, 17% strand | K4L7X3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.82 | 0.84 | 77 | FAD, GOL |
| 2 | 843 | 0.80 | 0.83 | 79 | FAD, GOL |
| 3 | 345 | 0.61 | 0.78 | 35 | empty |
| 4 | 119 | 0.41 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2411 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 5AF7 · 3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis… · the same entry in another collection · chain A against A, TM-score 1.00
- K4L7X3 · AlphaFold monomer V2.0 prediction for 3-sulfinopropanoyl-CoA desulfinase (K4L7X3) · a predicted model of the same protein · chain B 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 K4L7X3
- Elsewhere: RCSB PDB 5AF7 · PDBe 5AF7 · UniProt K4L7X3
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