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Structure of P450SKY (CYP163B3), a cytochrome P450 from skyllamycin biosynthesis in complex with a peptidyl carrier protein domain
Analyse Structure of P450SKY (CYP163B3), a cytochrome P450 from skyllamycin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PXH
- Type
- protein
- Length
- 1,456 residues
- Chains
- 6
- 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
- 15 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P450 monooxygenase (EC 1.14.14.1) | protein | 417 | 52% helix, 14% strand | F2YRY7 |
| B | Peptide synthetase | protein | 75 | 56% helix, 0% strand | F2YRY5 |
| C | P450 monooxygenase (EC 1.14.14.1) | protein | 409 | 52% helix, 13% strand | F2YRY7 |
| D, F | Peptide synthetase | protein | 74 | 58% helix, 0% strand | F2YRY5 |
| E | P450 monooxygenase (EC 1.14.14.1) | protein | 407 | 53% helix, 14% strand | F2YRY7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, C, E
- KH4 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] 1H-imidazole-4-carbothioate · ligand · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.85 | 0.89 | 64 | HEM, KH4 |
| 2 | 633 | 0.85 | 0.89 | 64 | HEM, KH4 |
| 3 | 880 | 0.85 | 0.86 | 88 | HEM, KH4 |
| 4 | 950 | 0.72 | 0.76 | 85 | empty |
| 5 | 338 | 0.68 | 0.82 | 29 | empty |
Interfaces
5 interfaces between chains.
- E–F · 689 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 683 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 674 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 655 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 221 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4PXH · 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 4PXH · PDBe 4PXH · UniProt F2YRY7 · UniProt F2YRY5
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