› 8yds

X-ray diffraction
1.9Å resolution

Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike protein in complex with Ce59

Released:
DOI: 10.2210/pdb8yds/pdb
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PDB entry 8yds coloured by chain, front view.
PDB entry 8yds coloured by chain, side view.
PDB entry 8yds coloured by chain, top view.
Source organisms:
Entry authors: Nakamura S, Numoto N, Fujiyoshi Y

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-283890 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
SARS-CoV-2 inhibiting peptide Ce59 Chain: A
Molecule details ›
Chain: A
Length: 39 amino acids
Theoretical weight: 4.82 KDa
Source organism: synthetic construct
Expression system: Not provided
Spike protein S1 Chain: B
Molecule details ›
Chain: B
Length: 230 amino acids
Theoretical weight: 26.27 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 333-526; Coverage: 15%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL45XU
Spacegroup: P3121
Unit cell:
a: 74.05Å b: 74.05Å c: 101Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.186 0.184 0.226
Expression systems:
  • Not provided
  • Homo sapiens

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