MolNFT v1 · #33104 · protein
Crystal structure of yc-17-bound cytochrome P450 pikc ( CYP107L1)
2CA0 · Cytochrome P450 monooxygenase: “Crystal structure of yc-17-bound cytochrome P450 pikc ( CYP107L1)”. X-ray diffraction, 2 ligands (HEM, PXI), 6 pockets (best druggability 0.86). MolNFT v1 #33104 on GenesisL1: 3D structure, binding…
- PDB
- 2CA0
- Type
- protein
- Length
- 786 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 monooxygenase
- UniProt
- O87605
- Ligands
- HEM, PXI
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome P450 monooxygenase | protein | 393 | 47% helix, 9% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.86 | 0.88 | 83 | HEM, PXI |
| 2 | 901 | 0.86 | 0.88 | 80 | HEM, PXI |
| 3 | 1084 | 0.80 | 0.81 | 94 | empty |
| 4 | 56 | 0.61 | 0.92 | 13 | empty |
| 5 | 57 | 0.36 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 436 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2CA0 · 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 2CA0 · PDBe 2CA0 · UniProt O87605
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