MolNFT v1 · #170389 · protein
Crystal structure of the envelope glycoprotein complex of andes virus in a near postfusion conformation
6Y5W · Envelope POLYPROTEIN,ENVELOPE polyprotein: “Crystal structure of the envelope glycoprotein complex of andes virus in a near postfusion conformation”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 5 pockets (best druggability 0.80).…
- PDB
- 6Y5W
- Type
- protein
- Length
- 754 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
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope POLYPROTEIN,ENVELOPE polyprotein | protein | 349 | 11% helix, 44% strand | A0A3Q8TA45 |
| B | Envelope POLYPROTEIN,ENVELOPE polyprotein | protein | 405 | 5% helix, 57% strand | A0A3Q8TA45 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.80 | 0.81 | 107 | empty |
| 2 | 185 | 0.59 | 0.81 | 38 | empty |
| 3 | 208 | 0.55 | 0.79 | 33 | empty |
| 4 | 190 | 0.52 | 0.78 | 30 | empty |
| 5 | 275 | 0.50 | 0.74 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1773 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6Y5W · Crystal structure of the envelope glycoprotein complex of Andes virus in a near… · 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 6Y5W · PDBe 6Y5W · UniProt A0A3Q8TA45
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