Research workbench
Prefusion structure of pedv spike
Analyse Prefusion structure of pedv spike in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U7K
- Type
- protein
- Length
- 3,192 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- Q91AV1
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1064 | 20% helix, 35% strand | Q91AV1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 69 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, C, B
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 | 920 | 0.88 | 0.91 | 102 | empty |
| 2 | 957 | 0.87 | 0.88 | 143 | empty |
| 3 | 647 | 0.80 | 0.85 | 89 | empty |
| 4 | 592 | 0.80 | 0.85 | 92 | empty |
| 5 | 507 | 0.79 | 0.86 | 68 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6091 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 6090 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 6070 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 glycan, 39 disulfide (N-glycosylation, disulfide, glycosylation, glycation).
Compared structures
- 6U7K · Prefusion structure of PEDV spike · 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 Q91AV1
- Elsewhere: RCSB PDB 6U7K · PDBe 6U7K · UniProt Q91AV1
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