MolNFT v1 · #32608 · protein
Ligand-free structure of cytochrome P450 pikc (CYP107L1)
2BVJ · Cytochrome P450 monooxygenase: “Ligand-free structure of cytochrome P450 pikc (CYP107L1)”. X-ray diffraction, 1 ligand (HEM), 7 pockets (best druggability 0.85). MolNFT v1 #32608 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2BVJ
- Type
- protein
- Length
- 785 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 monooxygenase
- UniProt
- O87605
- Ligands
- HEM
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 monooxygenase | protein | 394 | 53% helix, 10% strand | O87605 |
| B | Cytochrome P450 monooxygenase | protein | 391 | 51% helix, 10% strand | O87605 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.85 | 0.87 | 70 | HEM |
| 2 | 773 | 0.81 | 0.84 | 86 | HEM |
| 3 | 201 | 0.65 | 0.84 | 40 | empty |
| 4 | 403 | 0.63 | 0.77 | 50 | DTT |
| 5 | 71 | 0.57 | 0.88 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1251 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2BVJ · Ligand-free structure of cytochrome P450 PikC (CYP107L1) · the same entry in another collection · chain B against B, 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 2BVJ · PDBe 2BVJ · UniProt O87605
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