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Crystal structure of human respiratory syncytial virus fusion glycoprotein inhibitor escape variant K394R-S398L stabilized in the prefusion state
Analyse Crystal structure of human respiratory syncytial virus fusion glycoprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EAH
- Type
- protein
- Length
- 1,325 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0
- UniProt
- W8RJF9
- Ligands
- NAG, FUC, SO4
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion glycoprotein F0 | protein | 446 | 29% helix, 33% strand | W8RJF9 |
| B | Fusion glycoprotein F0 | protein | 440 | 30% helix, 34% strand | W8RJF9 |
| C | Fusion glycoprotein F0 | protein | 439 | 30% helix, 34% strand | W8RJF9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C
- FUC · alpha-L-fucopyranose · sugar · chains C
- SO4 · Sulfate ion · ion · 20 copies · chains A, C, B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.82 | 0.83 | 72 | empty |
| 2 | 469 | 0.81 | 0.89 | 53 | empty |
| 3 | 821 | 0.77 | 0.81 | 83 | SO4 |
| 4 | 562 | 0.74 | 0.82 | 51 | empty |
| 5 | 593 | 0.73 | 0.81 | 58 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2521 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 2484 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2269 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6EAH · Crystal structure of human respiratory syncytial virus fusion glycoprotein inhibitor… · 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 W8RJF9
- Elsewhere: RCSB PDB 6EAH · PDBe 6EAH · UniProt W8RJF9
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