Research workbench
Cryo-EM MAP of ipec-J2 cell-derived pedv PT52 S protein one D0-down and two D0-up
Analyse Cryo-EM MAP of ipec-J2 cell-derived pedv PT52 S protein one D0-down and two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Y6T
- Type
- protein
- Length
- 3,446 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- A0A1Y0DD46
- Ligands
- NAG, BMA, FUC, MAN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1124 | 22% helix, 28% strand | A0A1Y0DD46 |
| C | Spike glycoprotein | protein | 1098 | 23% helix, 30% strand | A0A1Y0DD46 |
| B | Spike glycoprotein | protein | 1224 | 20% helix, 33% strand | A0A1Y0DD46 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 82 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 18 copies · chains A, C, B
- FUC · alpha-L-fucopyranose · sugar · 9 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A
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 | 951 | 0.88 | 0.90 | 115 | empty |
| 2 | 566 | 0.86 | 0.91 | 98 | empty |
| 3 | 555 | 0.83 | 0.88 | 79 | empty |
| 4 | 445 | 0.83 | 0.90 | 77 | empty |
| 5 | 431 | 0.82 | 0.90 | 62 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5040 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 4920 Ų buried · 64 hydrogen bonds · protein-protein
- C–B · 4787 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 31 disulfide (N-glycosylation, disulfide).
Compared structures
- 7Y6T · Cryo-EM map of IPEC-J2 cell-derived PEDV PT52 S protein one D0-down and two D0-up · 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 7Y6T · PDBe 7Y6T · UniProt A0A1Y0DD46
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