Research workbench
Crystal structure of mouse prion protein complexed with chlorpromazine
Analyse Crystal structure of mouse prion protein complexed with chlorpromazine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MA8
- Type
- protein
- Length
- 539 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major prion protein; POM1 heavy chain; POM1 light chain
- UniProt
- P04925
- Ligands
- Z80
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Major prion protein | protein | 108 | 57% helix, 5% strand | P04925 |
| H | POM1 heavy chain | protein | 218 | 8% helix, 51% strand | — |
| L | POM1 light chain | protein | 213 | 6% helix, 50% strand | — |
Ligands and binding sites
- Z80 · 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.62 | 0.75 | 63 | empty |
| 2 | 202 | 0.51 | 0.77 | 37 | empty |
| 3 | 72 | 0.31 | 0.74 | 16 | empty |
| 4 | 59 | 0.28 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1734 Ų buried · 13 hydrogen bonds · protein-protein
- C–H · 418 Ų buried · 9 hydrogen bonds · protein-protein
- C–L · 265 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4MA8 · Crystal structure of mouse prion protein complexed with Chlorpromazine · the same entry in another collection · chain C against C, TM-score 1.00
- P04925 · AlphaFold monomer V2.0 prediction for major prion protein (P04925) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P04925
- Elsewhere: RCSB PDB 4MA8 · PDBe 4MA8 · UniProt P04925
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