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Crystal Structure of HIV-1 CAP256 RnS-3mut-2G-SOSIP.664 Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.5 Angstrom

X-ray diffraction
2.716Å resolution
PDB entry 6vzi coloured by chain, front view.
PDB entry 6vzi coloured by chain, side view.
PDB entry 6vzi coloured by chain, top view.
Source organisms:
Assembly composition:
hetero octadecamer (preferred)
Entry contents: 6 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero octadecamer
Accessible surface area: 160668.72 Å2
Buried surface area: 81157.01 Å2
Dissociation area: 16,483.58 Å2
Dissociation energy (ΔGdiss): -4.64 kcal/mol
Dissociation entropy (TΔSdiss): 160.67 kcal/mol
Symmetry number: 3
PDBe Complex ID: PDB-CPX-231537

Macromolecules

Transmembrane protein gp41
Chain: B
Length: 154 amino acids
Theoretical weight: 17.32 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: W6ICH7 (Residues: 504-657; Coverage: 18%)
Gene name: env
Pfam: Retroviral envelope protein
InterPro: Retroviral envelope protein GP41-like
Transmembrane protein gp41 in PDB entry 6vzi, assembly 1, front view.
Transmembrane protein gp41 in PDB entry 6vzi, assembly 1, side view.
Transmembrane protein gp41 in PDB entry 6vzi, assembly 1, top view.
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35O22 scFv heavy chain
Chain: D
Length: 134 amino acids
Theoretical weight: 14.66 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
35O22 scFv heavy chain in PDB entry 6vzi, assembly 1, front view.
35O22 scFv heavy chain in PDB entry 6vzi, assembly 1, side view.
35O22 scFv heavy chain in PDB entry 6vzi, assembly 1, top view.
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35O22 scFv light chain
Chain: E
Length: 114 amino acids
Theoretical weight: 12.36 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
35O22 scFv light chain in PDB entry 6vzi, assembly 1, front view.
35O22 scFv light chain in PDB entry 6vzi, assembly 1, side view.
35O22 scFv light chain in PDB entry 6vzi, assembly 1, top view.
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Envelope glycoprotein gp160
Chain: G
Length: 471 amino acids
Theoretical weight: 53.42 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: A0A0N9FF17 (Residues: 29-493; Coverage: 55%)
Gene name: env
Pfam: Envelope glycoprotein GP120
InterPro:
Envelope glycoprotein gp160 in PDB entry 6vzi, assembly 1, front view.
Envelope glycoprotein gp160 in PDB entry 6vzi, assembly 1, side view.
Envelope glycoprotein gp160 in PDB entry 6vzi, assembly 1, top view.
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3H109L Fab heavy chain
Chain: H
Length: 244 amino acids
Theoretical weight: 26.26 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
3H109L Fab heavy chain in PDB entry 6vzi, assembly 1, front view.
3H109L Fab heavy chain in PDB entry 6vzi, assembly 1, side view.
3H109L Fab heavy chain in PDB entry 6vzi, assembly 1, top view.
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3H109L Fab light chain
Chain: L
Length: 217 amino acids
Theoretical weight: 23.42 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
3H109L Fab light chain in PDB entry 6vzi, assembly 1, front view.
3H109L Fab light chain in PDB entry 6vzi, assembly 1, side view.
3H109L Fab light chain in PDB entry 6vzi, assembly 1, top view.
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