› 1yym

X-ray diffraction
2.2Å resolution

crystal structure of F23, 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/pdb1yym/pdb
PDB entry 1yym coloured by chain, front view.
PDB entry 1yym coloured by chain, side view.
PDB entry 1yym coloured by chain, top view.
Source organisms:
Primary publication:
Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth.
Huang CC, Stricher F, Martin L, Decker JM, Majeed S, Barthe P, Hendrickson WA, Robinson J, Roumestand C, Sodroski J, Wyatt R, Shaw GM, Vita C, Kwong PD
Structure 13 755-68 (2005)
PMID: 15893666

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)
Assembly name:
PDBe Complex ID:
PDB-CPX-233302 (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 1
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: Mus musculus
Structure domains: Immunoglobulins
antibody 17b heavy chain Chains: H, R
Molecule details ›
Chains: H, R
Length: 229 amino acids
Theoretical weight: 24.46 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
Structure domains: Immunoglobulins
F23, scorpion-toxin mimic of CD4 Chains: M, S
Molecule details ›
Chains: M, S
Length: 27 amino acids
Theoretical weight: 2.86 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand NAG 16 x NAG
Ligand EDO 2 x EDO
Ligand IPA 2 x IPA
1 modified residue:
Ligand VLM 2 x VLM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 51.62Å b: 157.041Å c: 108.929Å
α: 90° β: 93.45° γ: 90°
R-values:
R R work R free
0.209 0.209 0.268
Expression systems:
  • Drosophila melanogaster
  • Mus musculus
  • Not provided

Quick links

Citations

11 review citations

Engineering novel binding proteins from nonimmunoglobulin domains.
Binz et al. (2005)
10 more

10 mentions without citation

Search for allosteric disulfide bonds in NMR structures.
Schmidt et al. (2007)
9 more