Research workbench
Crystal structure of FAD-dependent dehydrogenase
Analyse Crystal structure of FAD-dependent dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CXT
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALPHA/BETA hydrolase fold protein; Butyryl-CoA dehydrogenase
- EC
- 1.3.8.1
- UniProt
- F2K074, F2K077
- Ligands
- FK4, FAD
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALPHA/BETA hydrolase fold protein | protein | 71 | 49% helix, 0% strand | F2K074 |
| B | Butyryl-CoA dehydrogenase (EC 1.3.8.1) | protein | 372 | 54% helix, 16% strand | F2K077 |
Ligands and binding sites
- FK4 · S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl] 1H-pyrrole-2-carbothioate · ligand · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.77 | 0.80 | 94 | FK4, FAD |
| 2 | 95 | 0.37 | 0.75 | 11 | empty |
| 3 | 60 | 0.36 | 0.79 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 790 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6CXT · Crystal structure of FAD-dependent dehydrogenase · 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 F2K074
- Every structure of UniProt F2K077
- Elsewhere: RCSB PDB 6CXT · PDBe 6CXT · UniProt F2K074 · UniProt F2K077
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