Research workbench
Cryo-EM MAP of pedv (pintung 52) S protein with all three protomers in the D0-down conformation determined in situ on intact viral particles.
Analyse Cryo-EM MAP of pedv (pintung 52) S protein with all three protomers in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W6M
- Type
- protein
- Length
- 3,672 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- A0A1Y0DD46
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1224 | 20% helix, 31% strand | A0A1Y0DD46 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 108 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 45 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 39 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.88 | 0.89 | 122 | empty |
| 2 | 666 | 0.86 | 0.90 | 100 | empty |
| 3 | 1000 | 0.86 | 0.86 | 114 | empty |
| 4 | 1029 | 0.86 | 0.86 | 117 | empty |
| 5 | 882 | 0.84 | 0.86 | 94 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4537 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 4519 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 4448 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7W6M · Cryo-EM map of PEDV (Pintung 52) S protein with all three protomers in the D0-down… · 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 A0A1Y0DD46
- Elsewhere: RCSB PDB 7W6M · PDBe 7W6M · UniProt A0A1Y0DD46
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