› 4dkq

X-ray diffraction
1.89Å resolution

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with DMJ-I-228

Released:
DOI: 10.2210/pdb4dkq/pdb
PDB entry 4dkq coloured by chain, front view.
PDB entry 4dkq coloured by chain, side view.
PDB entry 4dkq coloured by chain, top view.
Source organism: Human immunodeficiency virus type 1 (BRU ISOLATE)
Primary publication:
Structure-based design, synthesis, and characterization of dual hotspot small-molecule HIV-1 entry inhibitors.
LaLonde JM, Kwon YD, Jones DM, Sun AW, Courter JR, Soeta T, Kobayashi T, Princiotto AM, Wu X, Schön A, Freire E, Kwong PD, Mascola JR, Sodroski J, Madani N, Smith AB
J Med Chem 55 4382-96 (2012)
PMID: 22497421

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170898 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Envelope glycoprotein gp160 Chain: A
Molecule details ›
Chain: A
Length: 353 amino acids
Theoretical weight: 39.16 KDa
Source organism: Human immunodeficiency virus type 1 (BRU ISOLATE)
Expression system: Homo sapiens
UniProt:
  • Canonical: Q0ED31 (Residues: 43-486; Coverage: 41%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein

Ligands and Environments

3 bound ligands:
Ligand NAG 11 x NAG
Ligand EPE 1 x EPE
Ligand 0LK 1 x 0LK
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 63.741Å b: 67.523Å c: 89.255Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.192 0.233
Expression system: Homo sapiens

Quick links

Citations

8 review citations

Conformational Masking and Receptor-Dependent Unmasking of Highly Conserved Env Epitopes Recognized by Non-Neutralizing Antibodies That Mediate Potent ADCC against HIV-1.
Lewis et al. (2015)
7 more

8 mentions without citation

HIV-1 envelope glycoprotein structure.
Merk et al. (2013)
7 more