Research workbench
Selective oxidation of carbolide C-H bonds by engineered macrolide P450 monooxygenase
Analyse Selective oxidation of carbolide C-H bonds by engineered macrolide P450… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WI9
- Type
- protein
- Length
- 790 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 hydroxylase pikc
- UniProt
- O87605
- Ligands
- HEM, 1D2, SO4
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 hydroxylase pikc | protein | 396 | 51% helix, 10% strand | O87605 |
| B | Cytochrome P450 hydroxylase pikc | protein | 394 | 53% helix, 10% strand | O87605 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 1D2 · Cyclododecyl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.86 | 0.87 | 77 | HEM, 1D2 |
| 2 | 1103 | 0.84 | 0.85 | 81 | HEM, 1D2 |
| 3 | 816 | 0.74 | 0.79 | 59 | empty |
| 4 | 70 | 0.60 | 0.89 | 26 | empty |
| 5 | 190 | 0.48 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 442 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2WI9 · Selective oxidation of carbolide C-H bonds by engineered macrolide P450 monooxygenase · the same entry in another collection · chain A against A, TM-score 1.00
- O87605 · AlphaFold monomer V2.0 prediction for cytochrome P450 monooxygenase pikc (O87605) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O87605
- Elsewhere: RCSB PDB 2WI9 · PDBe 2WI9 · UniProt O87605
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