Research workbench
Machupo virus GP1 glycoprotein in complex with Fab fragment of antibody MAC1
Analyse Machupo virus GP1 glycoprotein in complex with Fab fragment of antibody MAC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QU1
- Type
- protein
- Length
- 589 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab MAC1 heavy chain; Fab MAC1 light chain; Pre-glycoprotein polyprotein gp complex
- UniProt
- Q6PXP4
- Ligands
- MAN, NAG, BMA
- Pockets
- 9 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab MAC1 heavy chain | protein | 222 | 7% helix, 51% strand | — |
| B | Fab MAC1 light chain | protein | 215 | 6% helix, 53% strand | — |
| C | Pre-glycoprotein polyprotein gp complex | protein | 152 | 28% helix, 22% strand | Q6PXP4 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 10 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.55 | 0.78 | 37 | empty |
| 2 | 80 | 0.48 | 0.83 | 25 | empty |
| 3 | 194 | 0.44 | 0.74 | 40 | GOL |
| 4 | 103 | 0.38 | 0.75 | 20 | GOL |
| 5 | 94 | 0.38 | 0.76 | 18 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1859 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 196 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7QU1 · Machupo virus GP1 glycoprotein in complex with Fab fragment of antibody MAC1 · 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 Q6PXP4
- Elsewhere: RCSB PDB 7QU1 · PDBe 7QU1 · UniProt Q6PXP4
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