MolNFT v1 · #103977 · protein
Structure of P450SKY (CYP163B3), a cytochrome P450 from skyllamycin biosynthesis in complex with a peptidyl carrier protein domain
4PWV · P450 monooxygenase: “Structure of P450SKY (CYP163B3), a cytochrome P450 from skyllamycin biosynthesis in complex with a peptidyl…”. X-ray diffraction, 2 ligands (HEM, KH4), 3 pockets (best druggability 0.85). MolNFT v1 #103977 on…
- PDB
- 4PWV
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P450 monooxygenase; Peptide synthetase
- EC
- 1.14.14.1
- UniProt
- F2YRY7, F2YRY5
- Ligands
- HEM, KH4
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P450 monooxygenase (EC 1.14.14.1) | protein | 411 | 50% helix, 13% strand | F2YRY7 |
| B | Peptide synthetase | protein | 75 | 56% helix, 0% strand | F2YRY5 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- KH4 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] 1H-imidazole-4-carbothioate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.85 | 0.89 | 68 | HEM, KH4 |
| 2 | 366 | 0.67 | 0.81 | 30 | empty |
| 3 | 233 | 0.55 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 701 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified, 1 covalent (engineered, covalent ligand).
Compared structures
- 4PWV · Structure of P450sky (CYP163B3), a cytochrome P450 from skyllamycin biosynthesis in… · 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 F2YRY7
- Every structure of UniProt F2YRY5
- Elsewhere: RCSB PDB 4PWV · PDBe 4PWV · UniProt F2YRY7 · UniProt F2YRY5
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