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Structure of sybody MR17 in complex with the SARS-CoV-2 S receptor-binding domain (RBD)

X-ray diffraction
2.77Å resolution
PDB entry 7c8w coloured by chain, front view.
PDB entry 7c8w coloured by chain, side view.
PDB entry 7c8w coloured by chain, top view.
Source organisms:
Assembly composition:
hetero dimer (preferred)
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Spike protein S2' and IG-heavy chain
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Multimeric state: hetero dimer
Accessible surface area: 15431.31 Å2
Buried surface area: 3029.88 Å2
Dissociation area: 895.24 Å2
Dissociation energy (ΔGdiss): -3.24 kcal/mol
Dissociation entropy (TΔSdiss): 11.57 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-209707

Macromolecules

Synthetic nanobody MR17
Chain: A
Length: 122 amino acids
Theoretical weight: 13.43 KDa
Source organism: synthetic construct
Expression system: Escherichia coli BL21(DE3)
InterPro:
Synthetic nanobody MR17 in PDB entry 7c8w, assembly 1, front view.
Synthetic nanobody MR17 in PDB entry 7c8w, assembly 1, side view.
Synthetic nanobody MR17 in PDB entry 7c8w, assembly 1, top view.
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Spike protein S1
Chain: B
Length: 213 amino acids
Theoretical weight: 23.75 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P0DTC2 (Residues: 330-531; Coverage: 16%)
Gene names: 2, S
Pfam: Betacoronavirus spike glycoprotein S1, receptor binding
InterPro:
Spike protein S1 in PDB entry 7c8w, assembly 1, front view.
Spike protein S1 in PDB entry 7c8w, assembly 1, side view.
Spike protein S1 in PDB entry 7c8w, assembly 1, top view.
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