Research workbench
FAD-dependent oxidoreductase from chaetomium thermophilum in complex with fragment 2-(1H-indol-3-yl)-N-[(1-methyl-1H-pyrrol-2-yl) METHYL]ETHANAMINE
Analyse FAD-dependent oxidoreductase from chaetomium thermophilum in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZE5
- 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
- 4AQ, FDA, NAG, MG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | FAD-dependent oxidoreductase | protein | 585 | 35% helix, 20% strand | — |
Ligands and binding sites
- 4AQ · 2-(1H-indol-3-yl)-N-[(1-methyl-1H-pyrrol-2-yl) methyl]ethanamine · 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 · 2 copies · 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 | 782 | 0.83 | 0.86 | 97 | FDA, 4AQ, FMT |
| 2 | 786 | 0.82 | 0.85 | 98 | FDA, 4AQ, FMT |
| 3 | 209 | 0.68 | 0.85 | 37 | empty |
| 4 | 79 | 0.59 | 0.89 | 28 | MG |
| 5 | 135 | 0.40 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 907 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ZE5 · 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 6ZE5 · PDBe 6ZE5
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