MolNFT v1 · #186057 · protein
Machupo virus GP1 glycoprotein in complex with Fab fragment of antibody MAC1
7QU1 · Fab MAC1 heavy chain: “Machupo virus GP1 glycoprotein in complex with Fab fragment of antibody MAC1”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 9 pockets (best druggability 0.55). MolNFT v1 #186057 on GenesisL1: 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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