Research workbench
Crystal structure of P450 2B6 (Y226H/K262R) in complex with two molecules of amlodipine
Analyse Crystal structure of P450 2B6 (Y226H/K262R) in complex with two molecules of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UA5
- Type
- protein
- Length
- 927 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2B6
- EC
- 1.14.14.1
- UniProt
- P20813
- Ligands
- 06X, HEM
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2B6 (EC 1.14.14.1) | protein | 465 | 52% helix, 7% strand | P20813 |
| B | Cytochrome P450 2B6 (EC 1.14.14.1) | protein | 462 | 52% helix, 7% strand | P20813 |
Ligands and binding sites
- 06X · Amlodipine · ligand · 4 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
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 | 1113 | 0.88 | 0.89 | 97 | HEM, 06X |
| 2 | 1101 | 0.87 | 0.88 | 101 | HEM, 06X |
| 3 | 141 | 0.76 | 0.93 | 28 | empty |
| 4 | 920 | 0.74 | 0.77 | 88 | empty |
| 5 | 148 | 0.72 | 0.90 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 889 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3UA5 · Crystal Structure of P450 2B6 (Y226H/K262R) in complex with two molecules of Amlodipine · 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 0.96
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 3UA5 · PDBe 3UA5 · UniProt P20813
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