Research workbench
V308E mutant of cytochrome P450 2D6 complexed with prinomastat
Analyse V308E mutant of cytochrome P450 2D6 complexed with prinomastat in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CSD
- Type
- protein
- Length
- 916 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2D6
- EC
- 1.14.14.1
- UniProt
- P10635
- Ligands
- HEM, PN0, CPS, ZN
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 462 | 52% helix, 10% strand | P10635 |
| B | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 454 | 54% helix, 10% strand | P10635 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PN0 · Prinomastat · ligand · 2 copies · chains A, B
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.88 | 0.94 | 60 | HEM, PN0 |
| 2 | 490 | 0.87 | 0.93 | 59 | HEM, PN0 |
| 3 | 1069 | 0.82 | 0.83 | 81 | empty |
| 4 | 564 | 0.73 | 0.81 | 39 | CPS |
| 5 | 497 | 0.67 | 0.78 | 32 | CPS |
Interfaces
1 interface between chains.
- A–B · 748 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 P10635
- Elsewhere: RCSB PDB 6CSD · PDBe 6CSD · UniProt P10635
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