Research workbench
Human prion protein (PrP) fragment 119-231 (G127V M129 variant) complexed to ICSM 18 (anti-Prp therapeutic antibody) Fab fragment
Analyse Human prion protein (PrP) fragment 119-231 (G127V M129 variant) complexed to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SV2
- Type
- protein
- Length
- 519 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens; Mus musculus
- Molecule
- Icsm 18-anti-prp therapeutic Fab light chain; Icsm 18-anti-prp therapeutic Fab heavy…
- UniProt
- P04156
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · resolution 2.3 · 3 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Icsm 18-anti-prp therapeutic Fab light chain | protein | 210 | 6% helix, 51% strand | — |
| H | Icsm 18-anti-prp therapeutic Fab heavy chain | protein | 208 | 6% helix, 55% strand | — |
| A | Major prion protein | protein | 101 | 63% helix, 4% strand | P04156 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.59 | 0.74 | 64 | empty |
| 2 | 58 | 0.27 | 0.73 | 11 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1594 Ų buried · 14 hydrogen bonds · protein-protein
- H–A · 594 Ų buried · 12 hydrogen bonds · protein-protein
- L–A · 387 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6SV2 · Human prion protein (prp) fragment 119-231 (G127V M129 variant) complexed to icsm 18… · the same entry in another collection · chain A against A, TM-score 1.00
- P04156 · AlphaFold monomer V2.0 prediction for major prion protein (P04156) · a predicted model of the same protein · chain A 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 P04156
- Elsewhere: RCSB PDB 6SV2 · PDBe 6SV2 · UniProt P04156
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