7f5g

X-ray diffraction
1.75Å resolution

The crystal structure of RBD-Nanobody complex, DL4 (SA4)

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-209763 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chains: A, C
Molecule details ›
Chains: A, C
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 DL4 Chains: B, D
Molecule details ›
Chains: B, D
Length: 146 amino acids
Theoretical weight: 16.19 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Unit cell:
a: 79.818Å b: 95.04Å c: 118.915Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.188 0.217
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli