Research workbench
Brain delivery of therapeutic proteins using an Fc fragment blood- brain barrier transport vehicle in mice and monkeys
Analyse Brain delivery of therapeutic proteins using an Fc fragment blood- brain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W3H
- Type
- protein
- Length
- 689 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atv Fc; Transferrin receptor protein 1,TRANSFERRIN receptor protein 1
- UniProt
- P02786
- Ligands
- NAG, MAN, BMA
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atv Fc | protein | 208 | 12% helix, 46% strand | — |
| C | Transferrin receptor protein 1,TRANSFERRIN receptor protein 1 | protein | 144 | 18% helix, 32% strand | P02786 |
| D | Transferrin receptor protein 1,TRANSFERRIN receptor protein 1 | protein | 147 | 18% helix, 30% strand | P02786 |
| B | Atv Fc | protein | 190 | 13% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.39 | 0.74 | 24 | empty |
| 2 | 109 | 0.38 | 0.75 | 23 | empty |
| 3 | 74 | 0.30 | 0.73 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1138 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 599 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 577 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6W3H · Brain delivery of therapeutic proteins using an Fc fragment blood-brain barrier transport… · the same entry in another collection · chain A against A, TM-score 1.00
- P02786 · AlphaFold monomer V2.0 prediction for transferrin receptor protein 1 (P02786) · a predicted model of the same protein · chain C against A, TM-score 0.63
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 P02786
- Elsewhere: RCSB PDB 6W3H · PDBe 6W3H · UniProt P02786
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