Research workbench
Structure of POM6 Fab fragment complexed with mouse prpc
Analyse Structure of POM6 Fab fragment complexed with mouse prpc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AQ7
- Type
- protein
- Length
- 530 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major prion protein; POM6 Fab heavy chain; POM6 Fab light chain
- UniProt
- P04925
- Ligands
- TCE
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major prion protein | protein | 100 | 61% helix, 4% strand | P04925 |
| H | POM6 Fab heavy chain | protein | 214 | 7% helix, 54% strand | — |
| L | POM6 Fab light chain | protein | 216 | 6% helix, 53% strand | — |
Ligands and binding sites
- TCE · 3,3',3''-phosphanetriyltripropanoic acid · ligand · chains H
- GOL · Glycerol · additive · 2 copies · chains A, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.63 | 0.74 | 56 | empty |
| 2 | 196 | 0.55 | 0.79 | 30 | empty |
| 3 | 180 | 0.50 | 0.77 | 25 | empty |
| 4 | 83 | 0.39 | 0.78 | 13 | empty |
| 5 | 73 | 0.36 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1671 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 537 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 375 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
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 6AQ7 · PDBe 6AQ7 · UniProt P04925
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