› 4dvr

X-ray diffraction
2.5Å resolution

Crystal structure of YU2 gp120 core in complex with Fab 48d and NBD-557

Released:
DOI: 10.2210/pdb4dvr/pdb
PDB entry 4dvr coloured by chain, front view.
PDB entry 4dvr coloured by chain, side view.
PDB entry 4dvr coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of HIV-1 gp120 envelope glycoprotein in complex with NBD analogues that target the CD4-binding site.
Kwon YD, LaLonde JM, Yang Y, Elban MA, Sugawara A, Courter JR, Jones DM, Smith AB, Debnath AK, Kwong PD
PLoS One 9 e85940 (2014)
PMID: 24489681

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-211126 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Surface protein gp120 Chain: G
Molecule details ›
Chain: G
Length: 313 amino acids
Theoretical weight: 34.92 KDa
Source organism: Human immunodeficiency virus type 1 (isolate YU2)
Expression system: Homo sapiens
UniProt:
  • Canonical: P35961 (Residues: 82-122, 195-297, 319-479; Coverage: 38%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
Fab 48d Light chain Chain: L
Molecule details ›
Chain: L
Length: 212 amino acids
Theoretical weight: 23.09 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Fab 48d Heavy chain Chain: H
Molecule details ›
Chain: H
Length: 219 amino acids
Theoretical weight: 23.39 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand NAG 7 x NAG
Ligand 0LY 1 x 0LY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 53.445Å b: 109.738Å c: 130.682Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.228 0.289
Expression system: Homo sapiens

Quick links

Citations

10 review citations

Development of Small-molecule HIV Entry Inhibitors Specifically Targeting gp120 or gp41.
Lu et al. (2016)
9 more

8 mentions without citation

On the irrationality of rational design of an HIV vaccine in light of protein intrinsic disorder.
Uversky VN. (2021)
7 more