7f5h

X-ray diffraction
3Å resolution

The crystal structure of RBD-Nanobody complex, DL28 (SC4)

Released:
Model geometry
Fit model/data

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-279643 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 213 amino acids
Theoretical weight: 23.75 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P0DTC2 (Residues: 330-531; Coverage: 16%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Nanobody DL28 Chains: C, D
Molecule details ›
Chains: C, D
Length: 143 amino acids
Theoretical weight: 15.53 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, FUC
2 bound ligands:
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P6522
Unit cell:
a: 177.463Å b: 177.463Å c: 133.13Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.228 0.226 0.248
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli