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Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex
2Z65
Primary Citation
 
 
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  •   Molecular Description Hide
    Classification: Immune System
    Structure Weight: 98973.54
    Molecule: Toll-like receptor 4, Variable lymphocyte receptor B
    Polymer: 1 Type: protein Length: 276
    Chains: A, B
    Fragment: TV3, UNP residues 27-228(human), E5564, UNP residues 19-158(Inshore hagfish)
    Organism Eptatretus burgeri Homo sapiens
    Gene Name TLR4
    UniProtKB:   Protein Feature View | Search PDB | O00206  
    Molecule: Lymphocyte antigen 96
    Polymer: 2 Type: protein Length: 140
    Chains: C, D
    Organism Homo sapiens
    Gene Names LY96 ESOP1 MD2
    UniProtKB:   Protein Feature View | Search PDB | Q9Y6Y9  
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens, eptatretus burgeri   Taxonomy   Common Name: Human, inshore hagfish Expression System: Spodoptera frugiperda  
    Polymer: 2
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Spodoptera frugiperda  
    Polymer: 4
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    2Z62  the TV3 hybrid of human TLR4 and hagfish VLRB.61 
    2Z63  the TV8 hybrid of human TLR4 and hagfish VLRB.61 
    2Z64  the mouse TLR4 and mouse MD-2 complex 
    2Z66  the VT3 hybrid of human TLR4 and hagfish VLRB.61 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name Interactions
    BMA
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    Download      		BMA C6 H12 O6
    BETA-D-MANNOSE
    E55
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    Download      		E55 C66 H126 N2 O19 P2
    3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)- 3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC- 11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}- 2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO- ALPHA-D-GLUCOPYRANOSE
    NAG
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    Download      		NAG C8 H15 N O6
    N-ACETYL-D-GLUCOSAMINE
    		NAG:2Z65
    NDG
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    Download      		NDG C8 H15 N O6
    2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    E55
    Search 
    Download      		E55
    IC50: 1.5 nM (97) - data from BindingDB  
    N/Ain BindingMoad
    N/Ain PDBbind
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
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  Biological Assembly 1       
Biological assembly 1 generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Lee, J.-O.,  Kim, H.M.,  Park, B.S.

    Deposition:   2007-07-22
    Release:   2007-09-18
    Last Modified (REVDAT):   2011-07-13
     
  •   Revision History    Hide
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    2011-07-13
    Flag residual B-value
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   2.70
    R-Value: 0.240 (obs.)
    R-Free: 0.289
    Space Group: P 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 67.19 α = 90.00 
    b = 80.99 β = 93.01 
    c = 107.76 γ = 90.00