MolNFT v1 · #167783 · protein
Cryo-EM structure of porcine epidemic diarrhea virus (pedv) spike protein
6VV5 · Spike glycoprotein: “Cryo-EM structure of porcine epidemic diarrhea virus (pedv) spike protein”. Electron microscopy, 4 ligands (PAM, NAG, MAN), 20 pockets (best druggability 0.89). MolNFT v1 #167783 on GenesisL1: 3D structure…
- PDB
- 6VV5
- Type
- protein
- Length
- 3,291 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- S5RJN4
- Ligands
- PAM, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 1 distinct chain · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1097 | 21% helix, 36% strand | S5RJN4 |
Ligands and binding sites
- PAM · Palmitoleic acid · ligand · 6 copies · chains A, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 78 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 6 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 | 1046 | 0.89 | 0.91 | 153 | PAM |
| 2 | 660 | 0.87 | 0.91 | 92 | PAM |
| 3 | 620 | 0.86 | 0.91 | 83 | PAM |
| 4 | 343 | 0.83 | 0.92 | 59 | empty |
| 5 | 295 | 0.81 | 0.92 | 47 | PAM |
Interfaces
3 interfaces between chains.
- B–C · 5451 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 5448 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 5445 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 6VV5 · Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) 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 S5RJN4
- Elsewhere: RCSB PDB 6VV5 · PDBe 6VV5 · UniProt S5RJN4
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