› 2ny2

X-ray diffraction
2Å resolution

HIV-1 gp120 Envelope Glycoprotein (T123C, T257S, S334A, S375W, G431C) Complexed with CD4 and Antibody 17b

Released:
DOI: 10.2210/pdb2ny2/pdb
PDB entry 2ny2 coloured by chain, front view.
PDB entry 2ny2 coloured by chain, side view.
PDB entry 2ny2 coloured by chain, top view.
Source organisms:
Primary publication:
Structural definition of a conserved neutralization epitope on HIV-1 gp120.
Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, Xiang SH, Yang X, Zhang MY, Zwick MB, Arthos J, Burton DR, Dimitrov DS, Sodroski J, Wyatt R, Nabel GJ, Kwong PD
Nature 445 732-7 (2007)
PMID: 17301785

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-208491 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Surface protein gp120 Chain: A
Molecule details ›
Chain: A
Length: 317 amino acids
Theoretical weight: 35.17 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: P19551 (Residues: 83-490; Coverage: 39%)
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: 184 amino acids
Theoretical weight: 20.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01730 (Residues: 26-208; Coverage: 42%)
Gene name: CD4
Sequence domains:
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 214 amino acids
Theoretical weight: 23.4 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q6P5S8 (Residues: 21-114, 115-234; Coverage: 99%)
Gene name: IGK@
Sequence domains:
Structure domains: Immunoglobulins
ANTIBODY 17B, HEAVY CHAIN Chain: D
Molecule details ›
Chain: D
Length: 229 amino acids
Theoretical weight: 24.46 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
3 bound ligands:
Ligand NAG 11 x NAG
Ligand EDO 2 x EDO
Ligand HEZ 1 x HEZ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P2221
Unit cell:
a: 71.605Å b: 88.024Å c: 196.016Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.194 0.223
Expression systems:
  • Homo sapiens
  • Escherichia coli

Quick links

Citations

113 review citations

HIV-1 neutralizing antibodies: understanding nature's pathways.
Mascola et al. (2013)
112 more

2 mentions without citation

HIV-1 antiretroviral drug therapy.
Arts et al. (2012)
1 more