› 6yz5

X-ray diffraction
1.8Å resolution

H11-D4 complex with SARS-CoV-2 RBD

Released:
DOI: 10.2210/pdb6yz5/pdb
PDB entry 6yz5 coloured by chain, front view.
PDB entry 6yz5 coloured by chain, side view.
PDB entry 6yz5 coloured by chain, top view.
Source organisms:
Entry authors: Naismith JH, Huo J, Mikolajek H, Ward P, Dumoux M, Owens RJ, Le Bas A

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-209681 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Spike protein S1 Chain: E
Molecule details ›
Chain: E
Length: 210 amino acids
Theoretical weight: 23.72 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DTC2 (Residues: 330-532; Coverage: 16%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Nanobody H11-D4 Chain: F
Molecule details ›
Chain: F
Length: 134 amino acids
Theoretical weight: 15.01 KDa
Source organism: Lama glama
Expression system: Escherichia coli

Ligands and Environments

3 bound ligands:
Ligand NAG 1 x NAG
Ligand EDO 12 x EDO
Ligand ACT 4 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P3121
Unit cell:
a: 78.28Å b: 78.28Å c: 127.09Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.167 0.166 0.193
Expression system: Escherichia coli

Quick links