Research workbench
Machupo virus GP1 bound to human transferrin receptor 1
Analyse Machupo virus GP1 bound to human transferrin receptor 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KAS
- Type
- protein
- Length
- 789 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transferrin receptor protein 1; Glycoprotein
- UniProt
- P02786, Q8AZ57
- Ligands
- NAG, MAN, FUC, BMA, K, PO4
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transferrin receptor protein 1 | protein | 633 | 38% helix, 19% strand | P02786 |
| B | Glycoprotein | protein | 156 | 28% helix, 24% strand | Q8AZ57 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains B
- BMA · beta-D-mannopyranose · sugar
- K · Potassium ion · metal · chains A
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
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 | 992 | 0.79 | 0.81 | 85 | PO4 |
| 2 | 234 | 0.58 | 0.79 | 38 | empty |
| 3 | 84 | 0.42 | 0.79 | 18 | empty |
| 4 | 129 | 0.42 | 0.75 | 24 | NAG |
| 5 | 104 | 0.41 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1017 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, 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 P02786
- Every structure of UniProt Q8AZ57
- Elsewhere: RCSB PDB 3KAS · PDBe 3KAS · UniProt P02786 · UniProt Q8AZ57
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