Research workbench
Crystal structure of piee, the flavin-dependent monooxygenase involved in the biosynthesis of piericidin A1
Analyse Crystal structure of piee, the flavin-dependent monooxygenase involved in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U0P
- Type
- protein
- Length
- 3,481 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,4-dichlorophenol 6-monooxygenase
- UniProt
- W0C4C9
- Ligands
- FAD, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,4-dichlorophenol 6-monooxygenase | protein | 581 | 35% helix, 24% strand | W0C4C9 |
| B | 2,4-dichlorophenol 6-monooxygenase | protein | 579 | 35% helix, 26% strand | W0C4C9 |
| C | 2,4-dichlorophenol 6-monooxygenase | protein | 585 | 34% helix, 25% strand | W0C4C9 |
| D | 2,4-dichlorophenol 6-monooxygenase | protein | 578 | 34% helix, 25% strand | W0C4C9 |
| E | 2,4-dichlorophenol 6-monooxygenase | protein | 579 | 35% helix, 25% strand | W0C4C9 |
| F | 2,4-dichlorophenol 6-monooxygenase | protein | 579 | 35% helix, 25% strand | W0C4C9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 17 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 12 copies · chains A, F, B, C, D, E
- 1PE · Pentaethylene glycol · additive · 6 copies · chains A, B, C, D, 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 | 1003 | 0.86 | 0.88 | 93 | PGE |
| 2 | 955 | 0.86 | 0.88 | 97 | GOL, PGE |
| 3 | 900 | 0.86 | 0.88 | 92 | PGE, GOL |
| 4 | 783 | 0.85 | 0.88 | 95 | FAD, PGE, GOL |
| 5 | 1176 | 0.85 | 0.86 | 101 | PGE |
Interfaces
12 interfaces between chains.
- A–B · 1403 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1400 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1387 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 914 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 878 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6U0P · Crystal structure of PieE, the flavin-dependent monooxygenase involved in the… · 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
- Every structure of UniProt W0C4C9
- Elsewhere: RCSB PDB 6U0P · PDBe 6U0P · UniProt W0C4C9
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