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
2I5Y
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Viral Protein/immune System
    Structure Weight: 174976.24
    Molecule: Exterior membrane glycoprotein(GP120)
    Polymer: 1 Type: protein Length: 313
    Chains: G, P
    Fragment: CORE
    Organism: Human immunodeficiency virus
    Gene Name: env
    UniProtKB: Search PDB | P35961   Protein Feature View
    Molecule: Antibody 17B Light chain
    Polymer: 2 Type: protein Length: 214
    Chains: L, Q
    Fragment: ANTIGEN-BINDING FRAGMENT, FAB
    Organism: Homo sapiens
    Molecule: Antibody 17B Heavy chain
    Polymer: 3 Type: protein Length: 229
    Chains: H, R
    Fragment: ANTIGEN-BINDING FRAGMENT, FAB
    Organism: Homo sapiens
    UniProtKB: Search PDB | Q5EBM2   Protein Feature View
    Molecule: CD4M47, SCORPION-TOXIN MIMIC OF CD4
    Polymer: 4 Type: protein Length: 27
    Chains: M, S
    Organism: synthetic construct
     
  •   Structure Validation Hide

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  •   Source Hide
    Polymer: 1
    Scientific Name: Human immunodeficiency virus   Taxonomy   Expression System: Drosophila melanogaster  
    Polymer: 2
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Human herpesvirus 4  
    Polymer: 3
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Human herpesvirus 4  
    Polymer: 4
    Scientific Name: Synthetic construct (synthetic construct)   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1YYL   Crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b 
    1YYM   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 
    2I60   Crystal structure of [Phe23]M47, a scorpion-toxic mimic of CD4, in complex with HIV-1 YU2 GP120 envelope glycoprotein and anti-HIV-1 antibody 17B 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    NAG
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    NAG C8 H15 N O6
    N-ACETYL-D-GLUCOSAMINE
    NDG
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    NDG C8 H15 N O6
    2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    MPT
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    MPT C3 H6 O2 S nonPolymer
    DPR
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    DPR C5 H9 N O2 dPeptideLinking
    BIF
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    BIF C15 H15 N O2 PHE lPeptideLinking
    VLM
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    VLM C5 H12 N2 O lPeptideLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly 1       
Biological assembly 1 assigned by authors
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  •   Deposition Summary Hide
    Authors:   Huang, C.-C.,  Kwong, P.D.

    Deposition:   2006-08-26
    Release:   2006-10-10
    Last Modified (REVDAT):   2012-06-06
     
  •   Revision History    Hide
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    2012-06-06
    Function and keywords
    2011-07-13
    Non-polymer description
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.20
    R-Value: 0.214 (obs.)
    R-Free: 0.273
    Space Group: P 1 21 1
    Unit Cell:
      Length [Å] Angles [°]
    a = 51.44 α = 90.00 
    b = 158.16 β = 93.67 
    c = 109.93 γ = 90.00