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Structural basis for broad neutralization of ebolaviruses by an antibody targeting the glycoprotein fusion loop
Analyse Structural basis for broad neutralization of ebolaviruses by an antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EAY
- Type
- protein
- Length
- 747 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CA45 light chain; CA45 heavy chain; Envelope glycoprotein
- UniProt
- Q05320
- Ligands
- MAN, NAG, BMA
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | CA45 light chain | protein | 211 | 6% helix, 51% strand | — |
| H | CA45 heavy chain | protein | 202 | 1% helix, 41% strand | — |
| A | Envelope glycoprotein | protein | 113 | 35% helix, 12% strand | Q05320 |
| B | Envelope glycoprotein | protein | 221 | 11% helix, 36% strand | Q05320 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.66 | 0.84 | 35 | empty |
| 2 | 577 | 0.60 | 0.73 | 59 | empty |
| 3 | 337 | 0.58 | 0.77 | 59 | empty |
| 4 | 175 | 0.57 | 0.81 | 31 | empty |
| 5 | 145 | 0.53 | 0.80 | 38 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2373 Ų buried · 25 hydrogen bonds · protein-protein
- L–H · 1381 Ų buried · 5 hydrogen bonds · protein-protein
- H–A · 667 Ų buried · 7 hydrogen bonds · protein-protein
- H–B · 375 Ų buried · 2 hydrogen bonds · protein-protein
- L–A · 238 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6EAY · Structural Basis for Broad Neutralization of Ebolaviruses by an Antibody Targeting the… · the same entry in another collection · chain L against L, 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 Q05320
- Elsewhere: RCSB PDB 6EAY · PDBe 6EAY · UniProt Q05320
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