MolNFT v1 · #154969 · protein
Crystal structure of E447A M130G acyl-CoA dehydrogenase FADE5 mutant from mycobacteria smegmatis in complex with C16COA
6KSB: “Crystal structure of E447A M130G acyl-CoA dehydrogenase FADE5 mutant from mycobacteria smegmatis in complex…”. X-ray diffraction, 3 ligands (FAD, PLM, COA), 15 pockets (best druggability 0.87). MolNFT v1 #154969 on GenesisL1: 3D…
- PDB
- 6KSB
- Type
- protein
- Length
- 1,217 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, PLM, COA
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA dehydrogenase (EC 1.3.8.1) | protein | 608 | 62% helix, 13% strand | A0A0D6G5A8 |
| B | Acyl-CoA dehydrogenase (EC 1.3.8.1) | protein | 609 | 62% helix, 13% strand | A0A0D6G5A8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- COA · Coenzyme A · 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
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.87 | 0.93 | 89 | FAD, PLM |
| 2 | 557 | 0.87 | 0.93 | 91 | FAD, PLM |
| 3 | 115 | 0.70 | 0.91 | 20 | empty |
| 4 | 84 | 0.65 | 0.92 | 16 | empty |
| 5 | 69 | 0.53 | 0.86 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4297 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 6KSB · Crystal Structure of E447A M130G 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 6KSB · PDBe 6KSB · UniProt A0A0D6G5A8
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