MolNFT v1 · #55493 · protein
Snapshots of enzymatic baeyer-villiger catalysis: oxygen activation and intermediate stabilization: ARG337LYS mutant in complex with NADP
2YM1 · Phenylacetone monooxygenase: “Snapshots of enzymatic baeyer-villiger catalysis: oxygen activation and intermediate stabilization: ARG337LYS…”. X-ray diffraction, 3 ligands (FAD, NAP, OXY), 5 pockets (best druggability 0.87). MolNFT…
- PDB
- 2YM1
- Type
- protein
- Length
- 531 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylacetone monooxygenase
- EC
- 1.14.13.92
- UniProt
- Q47PU3
- Ligands
- FAD, NAP, OXY
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylacetone monooxygenase (EC 1.14.13.92) | protein | 531 | 36% helix, 18% strand | Q47PU3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- OXY · Oxygen molecule · ion · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- PGE · Triethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.87 | 0.88 | 115 | FAD, NAP, OXY, PGE |
| 2 | 92 | 0.44 | 0.79 | 22 | empty |
| 3 | 53 | 0.41 | 0.82 | 18 | empty |
| 4 | 58 | 0.32 | 0.77 | 17 | empty |
| 5 | 57 | 0.26 | 0.73 | 20 | empty |
Compared structures
- 2YM1 · SNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATION AND INTERMEDIATE… · the same entry in another collection · chain A against A, TM-score 1.00
- Q47PU3 · AlphaFold monomer V2.0 prediction for phenylacetone monooxygenase (Q47PU3) · 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 Q47PU3
- Elsewhere: RCSB PDB 2YM1 · PDBe 2YM1 · UniProt Q47PU3
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