MolNFT v1 · #171717 · protein
Chaetomium thermophilum FAD-dependent oxidoreductase in complex with 4-nitrophenol
6ZE7: “Chaetomium thermophilum FAD-dependent oxidoreductase in complex with 4-nitrophenol”. X-ray diffraction, 5 ligands (NPO, FDA, NAG), 5 pockets (best druggability 0.83). MolNFT v1 #171717 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ZE7
- Type
- protein
- Length
- 1,170 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-dependent oxidoreductase
- Ligands
- NPO, FDA, NAG, MG, NA
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD-dependent oxidoreductase | protein | 584 | 35% helix, 20% strand | — |
| B | FAD-dependent oxidoreductase | protein | 586 | 35% helix, 20% strand | — |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · 3 copies · chains A, B
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
- FMT · Formic acid · additive · 8 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.83 | 0.86 | 94 | FDA, NPO, FMT |
| 2 | 757 | 0.82 | 0.85 | 96 | FDA, NPO, FMT |
| 3 | 192 | 0.68 | 0.86 | 34 | empty |
| 4 | 118 | 0.40 | 0.75 | 16 | empty |
| 5 | 101 | 0.38 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 866 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ZE7 · Chaetomium thermophilum FAD-dependent oxidoreductase in complex with 4-nitrophenol · 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 6ZE7 · PDBe 6ZE7
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