› 6z2m

X-ray diffraction
2.71Å resolution

H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex

Released:
DOI: 10.2210/pdb6z2m/pdb
PDB entry 6z2m coloured by chain, front view.
PDB entry 6z2m coloured by chain, side view.
PDB entry 6z2m coloured by chain, top view.
Source organisms:
Entry authors: Naismith JH, Ren J, Zhou D, Zhao Y, Stuart DI

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-209683 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Spike protein S1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 197 amino acids
Theoretical weight: 22.12 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
CR3022 antibody Chains: B, H
Molecule details ›
Chains: B, H
Length: 216 amino acids
Theoretical weight: 22.87 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
CR3022 antibody Chains: C, L
Molecule details ›
Chains: C, L
Length: 219 amino acids
Theoretical weight: 24.19 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
nanobody D4 Chains: D, F
Molecule details ›
Chains: D, F
Length: 127 amino acids
Theoretical weight: 14.05 KDa
Source organism: Lama glama
Expression system: Escherichia coli

Ligands and Environments

1 bound ligand:
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21212
Unit cell:
a: 149.717Å b: 150.395Å c: 119.537Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.241
Expression systems:
  • Homo sapiens
  • Escherichia coli

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