Research workbench
Crystal structure of human respiratory syncytial virus fusion glycoprotein inhibitor escape variant 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
- 6EAI
- Type
- protein
- Length
- 1,293 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0
- UniProt
- W8RJF9
- Ligands
- NAG, SO4
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fusion glycoprotein F0 | protein | 429 | 31% helix, 34% strand | W8RJF9 |
| C | Fusion glycoprotein F0 | protein | 435 | 31% helix, 34% strand | W8RJF9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 6 copies · chains A, C, B
- TAR · D(-)-tartaric acid · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.82 | 0.87 | 68 | empty |
| 2 | 890 | 0.82 | 0.84 | 55 | empty |
| 3 | 734 | 0.75 | 0.80 | 81 | SO4, NHE |
| 4 | 805 | 0.75 | 0.79 | 75 | SO4 |
| 5 | 1040 | 0.74 | 0.77 | 78 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 2232 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 2218 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2122 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6EAI · 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 6EAI · PDBe 6EAI · UniProt W8RJF9
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