MolNFT v1 · #113514 · protein
3-sulfinopropionyl-coenzyme a (3SP-CoA) desulfinase from advenella mimgardefordensis DPN7T: holo crystal structure with the substrate analog succinyl-CoA
5AHS · Acyl-CoA dehydrogenase: “3-sulfinopropionyl-coenzyme a (3SP-CoA) desulfinase from advenella mimgardefordensis DPN7T: holo crystal…”. X-ray diffraction, 3 ligands (FAD, COA, SO4), 20 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5AHS
- Type
- protein
- Length
- 2,345 residues
- Chains
- 6
- 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, COA, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | Acyl-CoA dehydrogenase (EC 3.13.1.4) | protein | 391 | 53% helix, 17% strand | K4L7X3 |
| D | Acyl-CoA dehydrogenase (EC 3.13.1.4) | protein | 390 | 53% helix, 17% strand | K4L7X3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, E, F, D
- COA · Coenzyme A · ligand · 5 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · chains B, C, E
- SIN · Succinic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.83 | 0.89 | 74 | FAD, COA |
| 2 | 705 | 0.83 | 0.86 | 90 | FAD, COA |
| 3 | 867 | 0.82 | 0.85 | 69 | SO4 |
| 4 | 676 | 0.82 | 0.86 | 64 | empty |
| 5 | 690 | 0.82 | 0.86 | 78 | FAD, COA |
Interfaces
9 interfaces between chains.
- C–E · 2392 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 2380 Ų buried · 57 hydrogen bonds · protein-protein
- C–F · 1963 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 546 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 423 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5AHS · 3-Sulfinopropionyl-Coenzyme A (3SP-CoA) desulfinase from Advenella mimgardefordensis… · the same entry in another collection · chain F against F, TM-score 1.00
- K4L7X3 · AlphaFold monomer V2.0 prediction for 3-sulfinopropanoyl-CoA desulfinase (K4L7X3) · a predicted model of the same protein · chain D 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 5AHS · PDBe 5AHS · UniProt K4L7X3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.