MolNFT v1 · #154004 · protein
Cryo-EM structure of spike protein of feline infectious peritonitis virus strain UU4
6JX7 · Feline infectious peritonitis virus spike protein: “Cryo-EM structure of spike protein of feline infectious peritonitis virus strain UU4”. Electron microscopy, 4 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.88). MolNFT…
- PDB
- 6JX7
- Type
- protein
- Length
- 3,735 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Feline infectious peritonitis virus spike protein
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 19% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Feline infectious peritonitis virus spike protein | protein | 1245 | 19% helix, 27% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 135 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 48 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 33 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 3 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 | 787 | 0.88 | 0.91 | 109 | empty |
| 2 | 705 | 0.87 | 0.91 | 97 | empty |
| 3 | 525 | 0.85 | 0.91 | 71 | empty |
| 4 | 696 | 0.83 | 0.87 | 89 | empty |
| 5 | 546 | 0.83 | 0.89 | 72 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6502 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 6502 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 6499 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 81 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 6JX7 · Cryo-EM structure of spike protein of feline infectious peritonitis virus strain UU4 · 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
- Elsewhere: RCSB PDB 6JX7 · PDBe 6JX7
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