Research workbench
Molecular basis of the flavin-based electron-bifurcating caffeyl-CoA reductase reaction
Analyse Molecular basis of the flavin-based electron-bifurcating caffeyl-CoA reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FAH
- Type
- protein
- Length
- 2,064 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caffeyl-CoA reductase-etf complex subunit care; Caffeyl-CoA reductase-etf complex subunit…
- EC
- 1.3.1.108
- UniProt
- H6LGM8, H6LGM7, H6LGM6
- Ligands
- FAD, SF4, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caffeyl-CoA reductase-etf complex subunit care (EC 1.3.1.108) | protein | 389 | 27% helix, 22% strand | H6LGM8 |
| B, F | Caffeyl-CoA reductase-etf complex subunit card (EC 1.3.1.108) | protein | 262 | 28% helix, 25% strand | H6LGM7 |
| C, D | Caffeyl-CoA reductase-etf complex subunit carc (EC 1.3.1.108) | protein | 379 | 59% helix, 14% strand | H6LGM6 |
| E | Caffeyl-CoA reductase-etf complex subunit care (EC 1.3.1.108) | protein | 393 | 26% helix, 20% strand | H6LGM8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, C, D, B, E, F
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, E
- SO4 · Sulfate ion · ion · 7 copies · chains C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.84 | 0.88 | 70 | FAD, SO4 |
| 2 | 706 | 0.84 | 0.88 | 71 | FAD, SO4 |
| 3 | 1013 | 0.81 | 0.83 | 99 | FAD, SO4 |
| 4 | 819 | 0.79 | 0.83 | 74 | FAD |
| 5 | 292 | 0.74 | 0.86 | 43 | SF4 |
Interfaces
9 interfaces between chains.
- E–F · 3627 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3605 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1888 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 825 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 802 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6FAH · Molecular basis of the flavin-based electron-bifurcating caffeyl-CoA reductase reaction · the same entry in another collection · chain F against F, TM-score 1.00
- H6LGM6 · AlphaFold monomer V2.0 prediction for caffeyl-CoA reductase-etf complex subunit carc… · a predicted model of the same protein · chain C against A, TM-score 0.99
- H6LGM7 · AlphaFold monomer V2.0 prediction for caffeyl-CoA reductase-etf complex subunit card… · a predicted model of the same protein · chain F against A, TM-score 0.92
- H6LGM8 · AlphaFold monomer V2.0 prediction for caffeyl-CoA reductase-etf complex subunit care… · a predicted model of the same protein · chain A against A, TM-score 0.65
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 H6LGM8
- Every structure of UniProt H6LGM7
- Every structure of UniProt H6LGM6
- Elsewhere: RCSB PDB 6FAH · PDBe 6FAH · UniProt H6LGM8 · UniProt H6LGM7 · UniProt H6LGM6
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