Research workbench
Crystal structure of ancestral flavin-containing monooxygenase (fmo) 3-6
Analyse Crystal structure of ancestral flavin-containing monooxygenase (fmo) 3-6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SE3
- Type
- protein
- Length
- 3,168 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancestral flavin-containing monooxygenase (fmo) 3-6
- Ligands
- FAD, NAP, OXY
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B, C, E, F | Ancestral flavin-containing monooxygenase (fmo) 3-6 | protein | 528 | 35% helix, 17% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains D, A, B, C, E, F
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains D, A, B, C, E, F
- OXY · Oxygen molecule · ion · 6 copies · chains D, A, B, C, E, F
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 | 630 | 0.85 | 0.90 | 82 | empty |
| 2 | 631 | 0.85 | 0.90 | 73 | empty |
| 3 | 1075 | 0.85 | 0.86 | 99 | FAD, NAP, OXY |
| 4 | 1093 | 0.85 | 0.86 | 103 | FAD, NAP, OXY |
| 5 | 1117 | 0.85 | 0.86 | 96 | FAD, NAP, OXY |
Interfaces
9 interfaces between chains.
- A–E · 2165 Ų buried · 42 hydrogen bonds · protein-protein
- C–F · 2137 Ų buried · 42 hydrogen bonds · protein-protein
- D–B · 2123 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 339 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 335 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SE3 · Crystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 3-6 · the same entry in another collection · chain D against D, 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 6SE3 · PDBe 6SE3
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