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Nanobody/VHH domain 7D12 in complex with domain III of the extracellular region of EGFR, pH 3.5

X-ray diffraction
2.655Å resolution
PDB entry 4krm coloured by chain, front view.
PDB entry 4krm coloured by chain, side view.
PDB entry 4krm coloured by chain, top view.
Source organisms:
Assembly composition:
hetero dimer (preferred)
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1
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Assembly Name: Epidermal growth factor receptor and IG-heavy chain
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Multimeric state: hetero dimer
Accessible surface area: 14676.94 Å2
Buried surface area: 2918.53 Å2
Dissociation area: 700.76 Å2
Dissociation energy (ΔGdiss): -6.89 kcal/mol
Dissociation entropy (TΔSdiss): 11.57 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-208218
Assembly 2 (preferred)
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Assembly Name: Epidermal growth factor receptor and IG-heavy chain
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Multimeric state: hetero dimer
Accessible surface area: 14718.49 Å2
Buried surface area: 3240.64 Å2
Dissociation area: 795.2 Å2
Dissociation energy (ΔGdiss): -7.27 kcal/mol
Dissociation entropy (TΔSdiss): 11.59 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-208218
Assembly 3
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Assembly Name: Epidermal growth factor receptor and IG-heavy chain
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Multimeric state: hetero dimer
Accessible surface area: 14175.62 Å2
Buried surface area: 2996.21 Å2
Dissociation area: 709.41 Å2
Dissociation energy (ΔGdiss): -5.22 kcal/mol
Dissociation entropy (TΔSdiss): 11.51 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-208218
Assembly 4
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Assembly Name: Epidermal growth factor receptor and IG-heavy chain
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Multimeric state: hetero dimer
Accessible surface area: 14758.18 Å2
Buried surface area: 3053.63 Å2
Dissociation area: 761.36 Å2
Dissociation energy (ΔGdiss): -6.23 kcal/mol
Dissociation entropy (TΔSdiss): 11.61 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-208218
Assembly 5
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Assembly Name: Epidermal growth factor receptor and IG-heavy chain
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Multimeric state: hetero dimer
Accessible surface area: 14672.36 Å2
Buried surface area: 2986.25 Å2
Dissociation area: 712.56 Å2
Dissociation energy (ΔGdiss): -5.94 kcal/mol
Dissociation entropy (TΔSdiss): 11.58 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-208218
Assembly 6
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Assembly Name: Epidermal growth factor receptor and IG-heavy chain
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Multimeric state: hetero dimer
Accessible surface area: 14620.51 Å2
Buried surface area: 2978.11 Å2
Dissociation area: 710.99 Å2
Dissociation energy (ΔGdiss): -4.48 kcal/mol
Dissociation entropy (TΔSdiss): 11.57 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-208218

Macromolecules

Epidermal growth factor receptor
Chains: A, C, E, G, I, K
Length: 214 amino acids
Theoretical weight: 23.79 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P00533 (Residues: 335-538; Coverage: 17%)
Gene names: EGFR, ERBB, ERBB1, HER1
Pfam: Receptor L domain
InterPro:
CATH: Receptor L-domain
Epidermal growth factor receptor in PDB entry 4krm, assembly 2, front view.
Epidermal growth factor receptor in PDB entry 4krm, assembly 2, side view.
Epidermal growth factor receptor in PDB entry 4krm, assembly 2, top view.
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Nanobody/VHH domain 7D12
Chains: B, D, F, H, J, L
Length: 133 amino acids
Theoretical weight: 14.58 KDa
Source organism: Lama glama
Expression system: Escherichia coli
InterPro:
CATH: Immunoglobulins
Nanobody/VHH domain 7D12 in PDB entry 4krm, assembly 2, front view.
Nanobody/VHH domain 7D12 in PDB entry 4krm, assembly 2, side view.
Nanobody/VHH domain 7D12 in PDB entry 4krm, assembly 2, top view.
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