› 2i60

X-ray diffraction
2.4Å resolution

Crystal structure of [Phe23]M47, 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/pdb2i60/pdb
PDB entry 2i60 coloured by chain, front view.
PDB entry 2i60 coloured by chain, side view.
PDB entry 2i60 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)
Assembly name:
PDBe Complex ID:
PDB-CPX-211124 (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: Human gammaherpesvirus 4
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: Human gammaherpesvirus 4
Structure domains: Immunoglobulins
[PHE23]M47, SCORPION-TOXIN MIMIC OF CD4 Chains: M, S
Molecule details ›
Chains: M, S
Length: 27 amino acids
Theoretical weight: 2.95 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NAG 16 x NAG
Ligand IPA 2 x IPA
2 modified residues:
Ligand DPR 2 x DPR
Ligand VLM 2 x VLM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 51.439Å b: 157.765Å c: 109.846Å
α: 90° β: 93.74° γ: 90°
R-values:
R R work R free
0.215 0.215 0.281
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

6 mentions without citation

Combinatorial optimization of a CD4-mimetic miniprotein and cocrystal structures with HIV-1 gp120 envelope glycoprotein.
Stricher et al. (2008)
5 more