› 2i5y

X-ray diffraction
2.2Å resolution

Crystal structure of CD4M47, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 GP120 envelope glycoprotein and anti-HIV-1 antibody 17B

Released:
DOI: 10.2210/pdb2i5y/pdb
PDB entry 2i5y coloured by chain, front view.
PDB entry 2i5y coloured by chain, side view.
PDB entry 2i5y coloured by chain, top view.
Source organisms:
Primary publication:
Combinatorial optimization of a CD4-mimetic miniprotein and cocrystal structures with HIV-1 gp120 envelope glycoprotein.
Stricher F, Huang CC, Descours A, Duquesnoy S, Combes O, Decker JM, Kwon YD, Lusso P, Shaw GM, Vita C, Kwong PD, Martin L
J Mol Biol 382 510-24 (2008)
PMID: 18619974

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-211123 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Surface protein gp120 Chains: G, P
Molecule details ›
Chains: G, P
Length: 313 amino acids
Theoretical weight: 34.84 KDa
Source organism: Human immunodeficiency virus
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: P35961 (Residues: 82-126, 191-293, 325-479; Coverage: 37%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
Antibody 17B Light chain Chains: L, Q
Molecule details ›
Chains: L, Q
Length: 214 amino acids
Theoretical weight: 23.4 KDa
Source organism: Homo sapiens
Expression system: Human gammaherpesvirus 4
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chains: H, R
Molecule details ›
Chains: H, R
Length: 229 amino acids
Theoretical weight: 24.46 KDa
Source organism: Homo sapiens
Expression system: Human gammaherpesvirus 4
UniProt:
  • Canonical: Q5EBM2 (Residues: 20-130, 131-243; Coverage: 45%)
Sequence domains:
Structure domains: Immunoglobulins
CD4M47, SCORPION-TOXIN MIMIC OF CD4 Chains: M, S
Molecule details ›
Chains: M, S
Length: 27 amino acids
Theoretical weight: 3.02 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NAG 16 x NAG
3 modified residues:
Ligand DPR 2 x DPR
Ligand BIF 2 x BIF
Ligand VLM 2 x VLM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 51.437Å b: 158.16Å c: 109.933Å
α: 90° β: 93.67° γ: 90°
R-values:
R R work R free
0.214 0.214 0.273
Expression systems:
  • Drosophila melanogaster
  • Human gammaherpesvirus 4
  • Not provided

Quick links

Citations

7 review citations

Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
Rich et al. (2010)
6 more

11 mentions without citation

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