› 8gd3

X-ray diffraction
2.19Å resolution

Crystal Structure of HIV-1 LM/HT Clade A/E CRF01 GP120 Core in Complex with DL-I-101

Released:
DOI: 10.2210/pdb8gd3/pdb
PDB entry 8gd3 coloured by chain, front view.
PDB entry 8gd3 coloured by chain, side view.
PDB entry 8gd3 coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC.
Ding S, Tolbert WD, Zhu H, Lee D, Marchitto L, Higgins T, Zhao X, Nguyen D, Sherburn R, Richard J, Gendron-Lepage G, Medjahed H, Mohammadi M, Abrams C, Pazgier M, Smith AB, Finzi A
OpenAccess logo Viruses 15 (2023)
PMID: 37243271

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-102400 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Human immunodeficiency virus 1 envelope glycoprotein Gp120 domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 355 amino acids
Theoretical weight: 39.45 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: A0A0M3KKW9 (Residues: 1-353; Coverage: 100%)
Gene name: HIV-1 Env
Sequence domains: Envelope glycoprotein GP120

Ligands and Environments

4 bound ligands:
Ligand NAG 10 x NAG
Ligand EPE 1 x EPE
Ligand Z1Z 1 x Z1Z
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P212121
Unit cell:
a: 62.73Å b: 66.948Å c: 92.175Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.208 0.254
Expression system: Homo sapiens

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Citations

3 citation in other articles

Soluble CD4 and low molecular weight CD4-mimetic compounds sensitize cells to be killed by anti-HIV cytotoxic immunoconjugates.
Pincus et al. (2023)
2 more

2 mentions without citation

Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC.
Ding et al. (2023)
1 more