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Crystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Complex with Neutralizing Antibody VRC-PG05 that Targets the Center of the Silent Face on the Outer Domain of gp120

X-ray diffraction
2.382Å resolution
PDB entry 6bf4 coloured by chain, front view.
PDB entry 6bf4 coloured by chain, side view.
PDB entry 6bf4 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: Envelope glycoprotein gp160 and IG-heavy chain and IG-light kappa chain
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Multimeric state: hetero trimer
Accessible surface area: 35308.74 Å2
Buried surface area: 16243.08 Å2
Dissociation area: 2,086.89 Å2
Dissociation energy (ΔGdiss): -29.47 kcal/mol
Dissociation entropy (TΔSdiss): 14.04 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-230644
Assembly 2
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Assembly Name: Envelope glycoprotein gp160 and IG-heavy chain and IG-light kappa chain
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Multimeric state: hetero trimer
Accessible surface area: 35428.63 Å2
Buried surface area: 16461.78 Å2
Dissociation area: 2,093.17 Å2
Dissociation energy (ΔGdiss): -33.64 kcal/mol
Dissociation entropy (TΔSdiss): 14.03 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-230644

Macromolecules

Envelope glycoprotein gp160
Chains: A, G
Length: 344 amino acids
Theoretical weight: 38.22 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: D7S2G1 (Residues: 43-474; Coverage: 41%)
Gene name: env
Pfam: Envelope glycoprotein GP120
InterPro:
Envelope glycoprotein gp160 in PDB entry 6bf4, assembly 1, front view.
Envelope glycoprotein gp160 in PDB entry 6bf4, assembly 1, side view.
Envelope glycoprotein gp160 in PDB entry 6bf4, assembly 1, top view.
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VRC-PG05 Fab heavy chain
Chains: B, H
Length: 229 amino acids
Theoretical weight: 24.64 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
CATH: Immunoglobulins
VRC-PG05 Fab heavy chain in PDB entry 6bf4, assembly 1, front view.
VRC-PG05 Fab heavy chain in PDB entry 6bf4, assembly 1, side view.
VRC-PG05 Fab heavy chain in PDB entry 6bf4, assembly 1, top view.
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VRC-PG05 Fab light chain
Chains: C, L
Length: 219 amino acids
Theoretical weight: 24.33 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
CATH: Immunoglobulins
VRC-PG05 Fab light chain in PDB entry 6bf4, assembly 1, front view.
VRC-PG05 Fab light chain in PDB entry 6bf4, assembly 1, side view.
VRC-PG05 Fab light chain in PDB entry 6bf4, assembly 1, top view.
Molecule details ›

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