MolNFT v1 · #125016 · protein
Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1 (HKU1 1A-ctd, 1.9 ångström, molecular replacement)
5KWB: “Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1…”. X-ray diffraction, 4 ligands (NAG, GLC, FRU), 1 pocket (best druggability 0.45). MolNFT v1 #125016 on GenesisL1: 3D…
- PDB
- 5KWB
- Type
- protein
- Length
- 364 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- Q5MQD0
- Ligands
- NAG, GLC, FRU, MG
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 364 | 15% helix, 35% strand | Q5MQD0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- MG · Magnesium ion · metal · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.45 | 0.77 | 25 | empty |
Modifications
Observed in the structure: 11 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5KWB · Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human… · 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 Q5MQD0
- Elsewhere: RCSB PDB 5KWB · PDBe 5KWB · UniProt Q5MQD0
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