› 5cay

X-ray diffraction
3Å resolution

Envelope glycoprotein gp120 core from HIV type 2 bound to the first two domains of human soluble CD4 receptor

Released:
DOI: 10.2210/pdb5cay/pdb
PDB entry 5cay coloured by chain, front view.
PDB entry 5cay coloured by chain, side view.
PDB entry 5cay coloured by chain, top view.
Source organisms:
Primary publication:
Structure of an HIV-2 gp120 in Complex with CD4.
Davenport YW, West AP, Bjorkman PJ
J Virol 90 2112-8 (2016)
PMID: 26608312

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-134538 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Surface protein gp120 Chain: G
Molecule details ›
Chain: G
Length: 345 amino acids
Theoretical weight: 40.38 KDa
Source organism: Human immunodeficiency virus type 2 (ISOLATE ST)
Expression system: Homo sapiens
UniProt:
  • Canonical: P20872 (Residues: 33-486; Coverage: 41%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
T-cell surface glycoprotein CD4 Chain: B
Molecule details ›
Chain: B
Length: 190 amino acids
Theoretical weight: 21.25 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P01730 (Residues: 26-208; Coverage: 42%)
Gene name: CD4
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
1 bound ligand:
Ligand NAG 6 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: C2221
Unit cell:
a: 94.276Å b: 100.223Å c: 199.139Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.231 0.287
Expression systems:
  • Homo sapiens
  • Spodoptera frugiperda

Quick links

Citations

2 review citations

Antiviral lectins: Selective inhibitors of viral entry.
Mitchell et al. (2017)
1 more

5 mentions without citation

Structure of an HIV-2 gp120 in Complex with CD4.
Davenport et al. (2016)
4 more