Research workbench
Structure of POM1 Fab fragment complexed with human prpc fragment 120- 230
Analyse Structure of POM1 Fab fragment complexed with human prpc fragment 120- 230 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DGI
- Type
- protein
- Length
- 528 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
- P04156
- Ligands
- NA
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major prion protein | protein | 97 | 62% helix, 4% strand | P04156 |
| H | POM1 Fab heavy chain | protein | 218 | 7% helix, 53% strand | — |
| L | POM1 Fab light chain | protein | 213 | 6% helix, 51% 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 | 535 | 0.61 | 0.75 | 65 | empty |
| 2 | 235 | 0.51 | 0.75 | 36 | empty |
| 3 | 60 | 0.28 | 0.74 | 19 | empty |
| 4 | 64 | 0.28 | 0.73 | 15 | empty |
| 5 | 52 | 0.28 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1717 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 412 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 256 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4DGI · Structure of POM1 FAB fragment complexed with human PrPc Fragment 120-230 · the same entry in another collection · chain A against A, TM-score 1.00
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 4DGI · PDBe 4DGI · UniProt P04156
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