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Molecular basis for antibody-mediated neutralization of New World hemorrhagic fever mammarenaviruses
Analyse Molecular basis for antibody-mediated neutralization of New World hemorrhagic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EN2
- Type
- protein
- Length
- 572 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.821
- Source
- Junin mammarenavirus; Mus musculus
- Molecule
- GD01 heavy chain; GD01 light chain; Pre-glycoprotein polyprotein GP complex
- UniProt
- P26313
- Ligands
- NAG, MAN, BMA, CL
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.821 · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GD01 heavy chain | protein | 219 | 7% helix, 51% strand | — |
| B | GD01 light chain | protein | 212 | 6% helix, 50% strand | — |
| C | Pre-glycoprotein polyprotein GP complex | protein | 141 | 26% helix, 25% strand | P26313 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, C
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B
- BMA · beta-D-mannopyranose · sugar · chains B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.63 | 0.76 | 57 | empty |
| 2 | 187 | 0.52 | 0.78 | 30 | empty |
| 3 | 212 | 0.51 | 0.76 | 29 | NAG |
| 4 | 128 | 0.39 | 0.74 | 27 | empty |
| 5 | 114 | 0.37 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1958 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 742 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 350 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5EN2 · Molecular basis for antibody-mediated neutralization of new world hemorrhagic fever… · 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 P26313
- Elsewhere: RCSB PDB 5EN2 · PDBe 5EN2 · UniProt P26313
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