Research workbench
Crystal structure of CYP2B6 (Y226H/K262R) in complex with a monoterpene bornane
Analyse Crystal structure of CYP2B6 (Y226H/K262R) in complex with a monoterpene bornane in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UDA
- Type
- protein
- Length
- 921 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2B6
- EC
- 1.14.13.-
- UniProt
- P20813
- Ligands
- CM5, HEM, CAE
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2B6 (EC 1.14.13.-) | protein | 461 | 54% helix, 10% strand | P20813 |
| B | Cytochrome P450 2B6 (EC 1.14.13.-) | protein | 460 | 54% 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
- CAE · Camphane · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.87 | 0.94 | 49 | HEM, CAE |
| 2 | 444 | 0.86 | 0.93 | 52 | HEM, CAE |
| 3 | 1067 | 0.77 | 0.79 | 124 | CM5 |
| 4 | 77 | 0.66 | 0.92 | 15 | empty |
| 5 | 134 | 0.41 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 916 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5UDA · Crystal structure of CYP2B6 (Y226H/K262R) in complex with a monoterpene bornane · 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 B 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 5UDA · PDBe 5UDA · UniProt P20813
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