Research workbench
Structure of the human metapneumovirus fusion protein with neutralizing antibody identifies a pneumovirus antigenic site
Analyse Structure of the human metapneumovirus fusion protein with neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DAG
- Type
- protein
- Length
- 816 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0; Neutralizing antibody DS7 heavy chain; Neutralizing antibody DS7…
- UniProt
- G3KCK8, P01857, Q8N5F4
- Ligands
- NAG, MAN, BMA
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion glycoprotein F0 | protein | 383 | 20% helix, 30% strand | G3KCK8 |
| H | Neutralizing antibody DS7 heavy chain | protein | 220 | 3% helix, 51% strand | P01857 |
| L | Neutralizing antibody DS7 light chain | protein | 213 | 6% helix, 41% strand | Q8N5F4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, H
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.73 | 0.79 | 61 | empty |
| 2 | 257 | 0.62 | 0.81 | 42 | empty |
| 3 | 483 | 0.58 | 0.74 | 59 | empty |
| 4 | 214 | 0.57 | 0.79 | 31 | empty |
| 5 | 225 | 0.52 | 0.76 | 38 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1865 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 596 Ų buried · 2 hydrogen bonds · protein-protein
- A–L · 338 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4DAG · Structure of the Human Metapneumovirus Fusion Protein with Neutralizing Antibody… · 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 G3KCK8
- Every structure of UniProt P01857
- Every structure of UniProt Q8N5F4
- Elsewhere: RCSB PDB 4DAG · PDBe 4DAG · UniProt G3KCK8 · UniProt P01857 · UniProt Q8N5F4
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