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Crystal structure of the envelope glycoprotein prefusion complex of andes virus - mutant H953F
Analyse Crystal structure of the envelope glycoprotein prefusion complex of andes virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y5F
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope POLYPROTEIN,ENVELOPE polyprotein
- UniProt
- A0A3Q8TA45
- Ligands
- NAG, BMA, MAN, PO4
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope POLYPROTEIN,ENVELOPE polyprotein | protein | 353 | 11% helix, 44% strand | A0A3Q8TA45 |
| B | Envelope POLYPROTEIN,ENVELOPE polyprotein | protein | 417 | 5% helix, 54% strand | A0A3Q8TA45 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.65 | 0.77 | 64 | empty |
| 2 | 403 | 0.65 | 0.79 | 43 | empty |
| 3 | 262 | 0.61 | 0.80 | 26 | empty |
| 4 | 52 | 0.53 | 0.88 | 17 | empty |
| 5 | 137 | 0.49 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1581 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6Y5F · Crystal structure of the envelope glycoprotein prefusion complex of Andes virus - Mutant… · 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 A0A3Q8TA45
- Elsewhere: RCSB PDB 6Y5F · PDBe 6Y5F · UniProt A0A3Q8TA45
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