Research workbench
Structural characterization of the complex between alpha- naphthoflavone and human cytochrome P450 1B1 (CYP1B1)
Analyse Structural characterization of the complex between alpha- naphthoflavone and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PM0
- Type
- protein
- Length
- 459 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 1B1
- EC
- 1.14.14.1
- UniProt
- Q16678
- Ligands
- HEM, BHF
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 1B1 (EC 1.14.14.1) | protein | 459 | 54% helix, 10% strand | Q16678 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- BHF · 2-phenyl-4H-benzo[h]chromen-4-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.86 | 0.94 | 52 | HEM, BHF |
| 2 | 265 | 0.58 | 0.78 | 52 | empty |
| 3 | 138 | 0.47 | 0.77 | 18 | empty |
| 4 | 137 | 0.45 | 0.77 | 27 | empty |
| 5 | 111 | 0.44 | 0.78 | 17 | empty |
Compared structures
- 3PM0 · Structural Characterization of the Complex between Alpha-Naphthoflavone and Human… · the same entry in another collection · chain A against A, TM-score 1.00
- Q16678 · AlphaFold monomer V2.0 prediction for cytochrome P450 1B1 (Q16678) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q16678
- Elsewhere: RCSB PDB 3PM0 · PDBe 3PM0 · UniProt Q16678
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