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Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody K288.2

X-ray diffraction
2.33Å resolution
PDB entry 7tp3 coloured by chain, front view.
PDB entry 7tp3 coloured by chain, side view.
PDB entry 7tp3 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Spike protein S2' and IG-heavy chain and IG-light kappa chain
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Multimeric state: hetero trimer
Accessible surface area: 28264.7 Å2
Buried surface area: 6173.46 Å2
Dissociation area: 814.12 Å2
Dissociation energy (ΔGdiss): 0.81 kcal/mol
Dissociation entropy (TΔSdiss): 12.9 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-225200

Macromolecules

Spike protein S1
Chain: Z
Length: 231 amino acids
Theoretical weight: 26.1 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P0DTC2 (Residues: 319-541; Coverage: 18%)
Gene names: 2, S
Pfam: Betacoronavirus spike glycoprotein S1, receptor binding
InterPro:
Spike protein S1 in PDB entry 7tp3, assembly 1, front view.
Spike protein S1 in PDB entry 7tp3, assembly 1, side view.
Spike protein S1 in PDB entry 7tp3, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P0DTC2  
123120406080100120140160180200220
 
100200RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFSGHHHHHH
UniProt
P0DTC2
Chains
Domains
Secondary structure
Ligand binding sites
Sequence conservation
Molecule details ›

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K288.2 heavy chain
Chain: H
Length: 231 amino acids
Theoretical weight: 24.55 KDa
Source organism: Macaca mulatta
Expression system: Homo sapiens
InterPro:
K288.2 heavy chain in PDB entry 7tp3, assembly 1, front view.
K288.2 heavy chain in PDB entry 7tp3, assembly 1, side view.
K288.2 heavy chain in PDB entry 7tp3, assembly 1, top view.
123120406080100120140160180200220
 
100200EVRLVESGGGLVKPGGSLRLSCVASGFTFSSYEMHWVRQAPGKGLEWVSVISESGATTHYTDSVKGRFTISRDNAKNSLFLQMNSLRAEDTAVYYCTRPQSVTVFGVAATSYEAFDFWGQGLRVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC
Chains
RSRZ Outlier Chain B (auth H)
Chain B (auth H)
Domains
Secondary structure
Interaction interfaces
Sequence conservation
Molecule details ›

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K288.2 light chain
Chain: L
Length: 215 amino acids
Theoretical weight: 23.51 KDa
Source organism: Macaca mulatta
Expression system: Homo sapiens
InterPro:
K288.2 light chain in PDB entry 7tp3, assembly 1, front view.
K288.2 light chain in PDB entry 7tp3, assembly 1, side view.
K288.2 light chain in PDB entry 7tp3, assembly 1, top view.
121520406080100120140160180200
 
100200DIVMTQSPDTLSLSPGETATLSCRASQSVSSYVAWYQQKPEQPPRLLIYGSSSRATGMPDRFSGSGSGTDFTLTISSLEPDDFAVYYCQQYTNWPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS
Chains
RSRZ Outlier Chain C (auth L)
Chain C (auth L)
Domains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation
Molecule details ›

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