› 8rj7

X-ray diffraction
2.1Å resolution

The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29

Released:
DOI: 10.2210/pdb8rj7/pdb
PDB entry 8rj7 coloured by chain, front view.
PDB entry 8rj7 coloured by chain, side view.
PDB entry 8rj7 coloured by chain, top view.
Source organisms:
Entry authors: Casasnovas JM, Fernandez LA, Silva K

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-281517 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Spike protein S1 Chains: A, C, E, G, I
Molecule details ›
Chains: A, C, E, G, I
Length: 203 amino acids
Theoretical weight: 22.73 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 332-528; Coverage: 16%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Camel-derived nanobody 1.29 Chains: B, D, F, H, J
Molecule details ›
Chains: B, D, F, H, J
Length: 126 amino acids
Theoretical weight: 13.35 KDa
Source organism: Camelus dromedarius
Expression system: Homo sapiens

Ligands and Environments

3 bound ligands:
Ligand NAG 5 x NAG
Ligand SO4 5 x SO4
Ligand LYS 1 x LYS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P32
Unit cell:
a: 89.164Å b: 89.164Å c: 200.247Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.181 0.222
Expression system: Homo sapiens

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