Research workbench
Crystal structure of syrian hamster prion protein complexed with POM1 Fab
Analyse Crystal structure of syrian hamster prion protein complexed with POM1 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YXL
- Type
- protein
- Length
- 534 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major prion protein; POM1 Fab heavy chain; POM1 Fab light chain
- UniProt
- P04273
- Ligands
- NA
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major prion protein | protein | 103 | 59% helix, 4% strand | P04273 |
| H | POM1 Fab heavy chain | protein | 218 | 7% helix, 51% strand | — |
| L | POM1 Fab light chain | protein | 213 | 5% helix, 48% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.63 | 0.78 | 46 | empty |
| 2 | 564 | 0.62 | 0.75 | 68 | empty |
| 3 | 55 | 0.33 | 0.78 | 19 | empty |
| 4 | 81 | 0.33 | 0.74 | 19 | empty |
| 5 | 51 | 0.26 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1754 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 412 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 272 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4YXL · Crystal structure of Syrian hamster prion protein complexed with POM1 FAB · the same entry in another collection · chain A against A, TM-score 1.00
- P04273 · AlphaFold monomer V2.0 prediction for major prion protein (P04273) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P04273
- Elsewhere: RCSB PDB 4YXL · PDBe 4YXL · UniProt P04273
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