› › Structure analysis

SARS-CoV-2 Spike (6P) in complex with 1 R1-32 Fab

Electron Microscopy
4.75Å resolution
PDB entry 7ydy coloured by chain, front view.
PDB entry 7ydy coloured by chain, side view.
PDB entry 7ydy coloured by chain, top view.
Source organisms:
Assembly composition:
hetero pentamer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: SARS-CoV-2 post-fusion S2 Spike complex and antibody
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Multimeric state: hetero pentamer
Accessible surface area: 163718.05 Å2
Buried surface area: 44483.26 Å2
Dissociation area: 1,508.24 Å2
Dissociation energy (ΔGdiss): -1.19 kcal/mol
Dissociation entropy (TΔSdiss): 14.84 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-225409

Macromolecules

Spike glycoprotein
Chains: A, B, C
Length: 1208 amino acids
Theoretical weight: 133.78 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 1-1208; Coverage: 95%)
Gene names: 2, S
Pfam:
InterPro:
Spike glycoprotein in PDB entry 7ydy, assembly 1, front view.
Spike glycoprotein in PDB entry 7ydy, assembly 1, side view.
Spike glycoprotein in PDB entry 7ydy, assembly 1, top view.
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Heavy chain of R1-32 Fab
Chain: H
Length: 228 amino acids
Theoretical weight: 23.84 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
Heavy chain of R1-32 Fab in PDB entry 7ydy, assembly 1, front view.
Heavy chain of R1-32 Fab in PDB entry 7ydy, assembly 1, side view.
Heavy chain of R1-32 Fab in PDB entry 7ydy, assembly 1, top view.
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Light chain of R1-32 Fab
Chain: L
Length: 214 amino acids
Theoretical weight: 22.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
Light chain of R1-32 Fab in PDB entry 7ydy, assembly 1, front view.
Light chain of R1-32 Fab in PDB entry 7ydy, assembly 1, side view.
Light chain of R1-32 Fab in PDB entry 7ydy, assembly 1, top view.
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