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Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans
Analyse Structures of a deltacoronavirus spike protein bound to porcine and human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VPP
- Type
- protein
- Length
- 1,892 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase; Spike protein
- EC
- 3.4.11.-
- UniProt
- K7GMF9, A0A4P8D758
- Ligands
- NAG, ZN
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase (EC 3.4.11.-) | protein | 904 | 45% helix, 19% strand | K7GMF9 |
| B | Spike protein | protein | 90 | 0% helix, 48% strand | A0A4P8D758 |
| C | Aminopeptidase (EC 3.4.11.-) | protein | 898 | 45% helix, 20% strand | K7GMF9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, C, B
- ZN · Zinc ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.81 | 0.82 | 105 | ZN, GOL |
| 2 | 1077 | 0.81 | 0.82 | 98 | GOL |
| 3 | 920 | 0.78 | 0.81 | 68 | empty |
| 4 | 652 | 0.73 | 0.80 | 63 | empty |
| 5 | 358 | 0.72 | 0.84 | 33 | empty |
Interfaces
2 interfaces between chains.
- A–B · 968 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 908 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 7VPP · Structures of a deltacoronavirus spike protein bound to porcine and human receptors… · 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 K7GMF9
- Every structure of UniProt A0A4P8D758
- Elsewhere: RCSB PDB 7VPP · PDBe 7VPP · UniProt K7GMF9 · UniProt A0A4P8D758
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