MolNFT v1 · #38376 · protein
Crystal structure of flavin-containing monooxygenase (FMO)FROM S.POMBE and substrate (methimazole) complex
2GVC: “Crystal structure of flavin-containing monooxygenase (FMO)FROM S.POMBE and substrate (methimazole) complex”. X-ray diffraction, 3 ligands (PEO, FAD, MMZ), 20 pockets (best druggability 0.86). MolNFT v1 #38376 on GenesisL1: 3D…
- PDB
- 2GVC
- Type
- protein
- Length
- 1,768 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monooxygenase
- UniProt
- Q9HFE4
- Ligands
- PEO, FAD, MMZ
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Monooxygenase | protein | 442 | 28% helix, 22% strand | Q9HFE4 |
Ligands and binding sites
- PEO · Hydrogen peroxide · ligand · 4 copies · chains A, B, D, E
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, D, E
- MMZ · 1-methyl-1,3-dihydro-2H-imidazole-2-thione · ligand · 4 copies · chains A, B, D, E
- GOL · Glycerol · additive · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.86 | 0.87 | 104 | PEO, FAD, MMZ |
| 2 | 970 | 0.86 | 0.87 | 101 | PEO, FAD, MMZ |
| 3 | 867 | 0.86 | 0.88 | 97 | PEO, FAD, MMZ |
| 4 | 836 | 0.86 | 0.88 | 93 | PEO, FAD, MMZ |
| 5 | 334 | 0.82 | 0.92 | 66 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1689 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1664 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 208 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2GVC · Crystal structure of flavin-containing monooxygenase (FMO)from S.pombe and substrate… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9HFE4 · AlphaFold monomer V2.0 prediction for thiol-specific monooxygenase (Q9HFE4) · a predicted model of the same protein · 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
- Every structure of UniProt Q9HFE4
- Elsewhere: RCSB PDB 2GVC · PDBe 2GVC · UniProt Q9HFE4
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