Research workbench
Crystal structure of a cytochrome P450 2A6 in complex with a monoterpene - sabinene.
Analyse Crystal structure of a cytochrome P450 2A6 in complex with a monoterpene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RUI
- Type
- protein
- Length
- 2,788 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2A6
- EC
- 1.14.13.-
- UniProt
- P11509
- Ligands
- HEM, SNE
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B, E, F | Cytochrome P450 2A6 (EC 1.14.13.-) | protein | 465 | 52% helix, 10% strand | P11509 |
| A, C | Cytochrome P450 2A6 (EC 1.14.13.-) | protein | 464 | 53% helix, 9% strand | P11509 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains D, A, B, C, E, F
- SNE · Sabinene · ligand · 6 copies · chains D, A, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.87 | 0.94 | 46 | HEM, SNE |
| 2 | 452 | 0.86 | 0.93 | 49 | HEM, SNE |
| 3 | 1047 | 0.86 | 0.87 | 97 | HEM, SNE |
| 4 | 421 | 0.86 | 0.93 | 42 | HEM, SNE |
| 5 | 408 | 0.86 | 0.93 | 44 | SNE, HEM |
Interfaces
6 interfaces between chains.
- A–C · 695 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 461 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 355 Ų buried · 0 hydrogen bonds · protein-protein
- D–B · 355 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 186 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RUI · Crystal structure of a cytochrome P450 2A6 in complex with a monoterpene - sabinene. · the same entry in another collection · chain F against F, TM-score 1.00
- P11509 · AlphaFold monomer V2.0 prediction for cytochrome P450 2A6 (P11509) · 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 P11509
- Elsewhere: RCSB PDB 4RUI · PDBe 4RUI · UniProt P11509
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