› 4i53

X-ray diffraction
2.5Å resolution

Crystal structure of clade C1086 HIV-1 gp120 core in complex with DMJ-II-121

Released:
DOI: 10.2210/pdb4i53/pdb
PDB entry 4i53 coloured by chain, front view.
PDB entry 4i53 coloured by chain, side view.
PDB entry 4i53 coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization.
Lalonde JM, Le-Khac M, Jones DM, Courter JR, Park J, Schön A, Princiotto AM, Wu X, Mascola JR, Freire E, Sodroski J, Madani N, Hendrickson WA, Smith AB
ACS Med Chem Lett 4 338-343 (2013)
PMID: 23667716

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-111575 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Envelope glycoprotein gp160 Chains: A, B
Molecule details ›
Chains: A, B
Length: 358 amino acids
Theoretical weight: 39.76 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: C6G099 (Residues: 39-478; Coverage: 42%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein

Ligands and Environments

3 bound ligands:
Ligand 1C1 2 x 1C1
Ligand NAG 13 x NAG
Ligand FMT 1 x FMT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4C
Spacegroup: C2221
Unit cell:
a: 67.45Å b: 127.67Å c: 192.9Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.255 0.254 0.273
Expression system: Homo sapiens

Quick links

Citations

6 review citations

Structure-based design, synthesis and validation of CD4-mimetic small molecule inhibitors of HIV-1 entry: conversion of a viral entry agonist to an antagonist.
Courter et al. (2014)
5 more

5 mentions without citation

Small Molecule HIV-1 Attachment Inhibitors: Discovery, Mode of Action and Structural Basis of Inhibition.
Lai YT. (2021)
4 more