Research workbench
Crystal structure of yc-17-bound cytochrome P450 pikc (CYP107L1)
Analyse Crystal structure of yc-17-bound cytochrome P450 pikc (CYP107L1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C6H
- Type
- protein
- Length
- 787 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 monooxygenase
- UniProt
- O87605
- Ligands
- HEM, PXI, SO4
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 monooxygenase | protein | 393 | 53% helix, 10% strand | O87605 |
| B | Cytochrome P450 monooxygenase | protein | 394 | 53% helix, 10% strand | O87605 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PXI · 4-{[4-(dimethylamino)-3-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-12-ethyl-3,5,7,11-tetramethyloxacyclododec-9-ene-2,8-dione · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.87 | 0.88 | 81 | HEM, PXI |
| 2 | 1031 | 0.86 | 0.87 | 83 | HEM, PXI |
| 3 | 50 | 0.48 | 0.86 | 12 | empty |
Compared structures
- 2C6H · Crystal structure of YC-17-bound cytochrome P450 PikC (CYP107L1) · 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 2C6H · PDBe 2C6H · UniProt O87605
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