Research workbench
Structure of an octapeptide repeat of the prion protein bound to the POM2 Fab antibody fragment
Analyse Structure of an octapeptide repeat of the prion protein bound to the POM2 Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J8R
- Type
- protein
- Length
- 876 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of POM2 Fab; Heavy chain of POM2 Fab; Major prion protein
- UniProt
- P04925
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light chain of POM2 Fab | protein | 209 | 7% helix, 53% strand | — |
| B, D | Heavy chain of POM2 Fab | protein | 220 | 7% helix, 50% strand | — |
| I | Major prion protein | protein | 9 | 0% helix, 11% strand | P04925 |
| C | Light chain of POM2 Fab | protein | 210 | 6% helix, 49% strand | — |
| J | Major prion protein | protein | 8 | 0% helix, 13% strand | P04925 |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.62 | 0.77 | 56 | empty |
| 2 | 292 | 0.53 | 0.75 | 38 | empty |
| 3 | 184 | 0.50 | 0.77 | 27 | empty |
| 4 | 255 | 0.50 | 0.74 | 37 | empty |
| 5 | 265 | 0.49 | 0.74 | 40 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1702 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1679 Ų buried · 13 hydrogen bonds · protein-protein
- D–J · 455 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 424 Ų buried · 4 hydrogen bonds · protein-protein
- B–I · 418 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4J8R · Structure of an octapeptide repeat of the prion protein bound to the POM2 Fab antibody… · the same entry in another collection · chain J against J, TM-score 1.00
- P04925 · AlphaFold monomer V2.0 prediction for major prion protein (P04925) · a predicted model of the same protein · chain J against A, TM-score 0.34
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 4J8R · PDBe 4J8R · UniProt P04925
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