Structure analysis

Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide

X-ray diffraction
2.36Å resolution
Assembly composition:
hetero dimer (preferred)
Entry contents: 2 distinct polypeptide molecules

Assemblies

Assembly 1
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Multimeric state: hetero dimer
Accessible surface area: 8024.06 Å2
Buried surface area: 723.6 Å2
Dissociation area: 253.33 Å2
Dissociation energy (ΔGdiss): -2.07 kcal/mol
Dissociation entropy (TΔSdiss): 4.42 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-275938
Assembly 2
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Multimeric state: hetero dimer
Accessible surface area: 8602.34 Å2
Buried surface area: 706.54 Å2
Dissociation area: 250.47 Å2
Dissociation energy (ΔGdiss): -1.85 kcal/mol
Dissociation entropy (TΔSdiss): 5.07 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-275938
Assembly 3
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Multimeric state: hetero dimer
Accessible surface area: 8645.89 Å2
Buried surface area: 1317.55 Å2
Dissociation area: 355.06 Å2
Dissociation energy (ΔGdiss): -4.14 kcal/mol
Dissociation entropy (TΔSdiss): 6.71 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-275938
Assembly 4 (preferred)
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Multimeric state: hetero dimer
Accessible surface area: 8488.7 Å2
Buried surface area: 972.33 Å2
Dissociation area: 299.88 Å2
Dissociation energy (ΔGdiss): -3.03 kcal/mol
Dissociation entropy (TΔSdiss): 4.95 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-275938

Macromolecules

Chains: A, B, C, D
Length: 166 amino acids
Theoretical weight: 18.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O14786 (Residues: 273-427; Coverage: 17%)
Gene names: NRP, NRP1, VEGF165R
Pfam: F5/8 type C domain
InterPro:

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Chains: E, F, G, H
Length: 7 amino acids
Theoretical weight: 859 Da
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Not provided
UniProt:
  • Canonical: P0DTC2 (Residues: 679-685; Coverage: 1%)
Gene names: 2, S

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