Research workbench
Structure of ICSM 18 (anti-Prp therapeutic antibody) Fab fragment complexed with human Prp fragment 119-231
Analyse Structure of ICSM 18 (anti-Prp therapeutic antibody) Fab fragment complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W9E
- Type
- protein
- Length
- 526 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- HOMO SAPIENS; MUS MUSCULUS
- Molecule
- Major prion protein; Icsm 18-anti-prp therapeutic Fab heavy chain; Icsm 18-anti-prp…
- UniProt
- P04156
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · resolution 2.9 · 3 distinct chains · 16% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major prion protein | protein | 99 | 63% helix, 4% strand | P04156 |
| H | Icsm 18-anti-prp therapeutic Fab heavy chain | protein | 215 | 4% helix, 52% strand | — |
| L | Icsm 18-anti-prp therapeutic Fab light chain | protein | 212 | 7% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.62 | 0.74 | 61 | empty |
| 2 | 154 | 0.46 | 0.76 | 28 | empty |
| 3 | 79 | 0.34 | 0.75 | 20 | empty |
| 4 | 72 | 0.32 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1763 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 570 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 395 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2W9E · Structure of icsm 18 (anti-prp therapeutic antibody) Fab fragment complexed with human… · 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 0.97
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 2W9E · PDBe 2W9E · UniProt P04156
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