Research workbench
Symmetry-expanded and locally refined protomer structure of ipec-J2 cell-derived pedv PT52 S with a ctd-close conformation
Analyse Symmetry-expanded and locally refined protomer structure of ipec-J2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Y6U
- Type
- protein
- Length
- 1,224 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- A0A1Y0DD46
- Ligands
- NAG, BMA, FUC, MAN
- Pockets
- 13 · best druggability 0.74
Structure
electron microscopy · 1 distinct chain · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1224 | 19% helix, 32% strand | A0A1Y0DD46 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.74 | 0.80 | 75 | empty |
| 2 | 290 | 0.69 | 0.83 | 36 | empty |
| 3 | 233 | 0.60 | 0.80 | 30 | empty |
| 4 | 81 | 0.51 | 0.84 | 19 | empty |
| 5 | 256 | 0.51 | 0.75 | 37 | empty |
Modifications
Observed in the structure: 18 glycan, 13 disulfide (N-glycosylation, disulfide).
Compared structures
- 7Y6U · Symmetry-expanded and locally refined protomer structure of IPEC-J2 cell-derived PEDV… · 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 7Y6U · PDBe 7Y6U · UniProt A0A1Y0DD46
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