MolNFT v1 · #106190 · protein
Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with (+)-3-carene
4RRT: “Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with (+)-3-carene”. X-ray diffraction, 3 ligands (CM5, HEM, 3V4), 11 pockets (best druggability 0.86). MolNFT v1 #106190 on GenesisL1: 3D structure, binding…
- PDB
- 4RRT
- Type
- protein
- Length
- 922 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2B6
- EC
- 1.14.13.-, 1.14.14.1
- UniProt
- P20813
- Ligands
- CM5, HEM, 3V4
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome P450 2B6 (EC 1.14.13.-, 1.14.14.1) | protein | 461 | 53% helix, 10% strand | P20813 |
Ligands and binding sites
- CM5 · 5-cyclohexyl-1-pentyl-beta-D-maltoside · ligand · 6 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 3V4 · (+)-3-carene · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.86 | 0.93 | 50 | HEM, 3V4 |
| 2 | 440 | 0.86 | 0.93 | 55 | HEM, 3V4 |
| 3 | 742 | 0.72 | 0.78 | 78 | CM5 |
| 4 | 540 | 0.72 | 0.81 | 62 | empty |
| 5 | 74 | 0.64 | 0.91 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 867 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4RRT · Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P20813 · AlphaFold monomer V2.0 prediction for cytochrome P450 2B6 (P20813) · a predicted model of the same protein · 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 P20813
- Elsewhere: RCSB PDB 4RRT · PDBe 4RRT · UniProt P20813
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