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Crystal structure of porcine hemagglutinating encephalomyelitis virus spike protein lectin domain
Analyse Crystal structure of porcine hemagglutinating encephalomyelitis virus spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QFY
- Type
- protein
- Length
- 572 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- A0A1Z2WUW0
- Ligands
- NAG, BMA
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 288 | 5% helix, 47% strand | A0A1Z2WUW0 |
| B | Spike glycoprotein | protein | 284 | 5% helix, 48% strand | A0A1Z2WUW0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.70 | 0.81 | 53 | empty |
| 2 | 54 | 0.40 | 0.82 | 17 | empty |
| 3 | 50 | 0.36 | 0.80 | 15 | empty |
| 4 | 69 | 0.29 | 0.72 | 14 | empty |
| 5 | 60 | 0.28 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 318 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6QFY · Crystal structure of porcine hemagglutinating encephalomyelitis virus spike protein… · 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 A0A1Z2WUW0
- Elsewhere: RCSB PDB 6QFY · PDBe 6QFY · UniProt A0A1Z2WUW0
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