MolNFT v1 · #171714 · protein
FAD-dependent oxidoreductase from chaetomium thermophilum in complex with fragment 4-oxo-N-[(1S)-1-(pyridin-3-YL)ETHYL]-4-(thiophen-2-yl) butanamide
6ZE4: “FAD-dependent oxidoreductase from chaetomium thermophilum in complex with fragment…”. X-ray diffraction, 6 ligands (FDA, 479, NAG), 6 pockets (best druggability 0.83). MolNFT v1 #171714 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ZE4
- Type
- protein
- Length
- 1,169 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-dependent oxidoreductase
- Ligands
- FDA, 479, NAG, BMA, NA, MG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD-dependent oxidoreductase | protein | 585 | 34% helix, 20% strand | — |
| B | FAD-dependent oxidoreductase | protein | 584 | 35% helix, 20% strand | — |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
- 479 · 4-oxo-N-[(1S)-1-(pyridin-3-yl)ethyl]-4-(thiophen-2-yl) butanamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- NA · Sodium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.83 | 0.86 | 97 | FDA, 479, FMT |
| 2 | 751 | 0.83 | 0.86 | 91 | FDA, 479, FMT |
| 3 | 203 | 0.67 | 0.85 | 36 | empty |
| 4 | 100 | 0.56 | 0.85 | 28 | MG |
| 5 | 120 | 0.38 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 900 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ZE4 · FAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment… · 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
- Elsewhere: RCSB PDB 6ZE4 · PDBe 6ZE4
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