MolNFT v1 · #154968 · protein
Crystal structure of E447A acyl-CoA dehydrogenase FADE5 mutant from mycobacteria smegmatis in complex with C18COA
6KSA: “Crystal structure of E447A acyl-CoA dehydrogenase FADE5 mutant from mycobacteria smegmatis in complex with…”. X-ray diffraction, 4 ligands (FAD, ST9, MG), 11 pockets (best druggability 0.89). MolNFT v1 #154968 on GenesisL1: 3D…
- PDB
- 6KSA
- Type
- protein
- Length
- 1,218 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase
- EC
- 1.3.8.1
- UniProt
- A0A0D6G5A8
- Ligands
- FAD, ST9, MG, SO4
- Pockets
- 11 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA dehydrogenase (EC 1.3.8.1) | protein | 607 | 62% helix, 13% strand | A0A0D6G5A8 |
| B | Acyl-CoA dehydrogenase (EC 1.3.8.1) | protein | 611 | 61% helix, 12% strand | A0A0D6G5A8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- ST9 · Stearoyl-coenzyme A · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.89 | 0.92 | 97 | FAD, ST9 |
| 2 | 574 | 0.87 | 0.93 | 83 | FAD, ST9 |
| 3 | 191 | 0.76 | 0.91 | 34 | empty |
| 4 | 61 | 0.56 | 0.88 | 16 | empty |
| 5 | 180 | 0.54 | 0.79 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 4342 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 6KSA · Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria… · 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 A0A0D6G5A8
- Elsewhere: RCSB PDB 6KSA · PDBe 6KSA · UniProt A0A0D6G5A8
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