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Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924
3GZN
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Protein Binding/ligase
    Structure Weight: 244268.50
    Molecule: NEDD8-activating enzyme E1 regulatory subunit
    Polymer: 1 Type: protein Length: 534
    Chains: A, C
    Organism: Homo sapiens
    Gene Names: Gene View for NAE1 APPBP1 HPP1
    UniProtKB: Protein Feature View | Search PDB | Q13564  
    Molecule: NEDD8-activating enzyme E1 catalytic subunit
    Polymer: 2 Type: protein Length: 463
    Chains: B, D
    EC#: 6.3.2   
    Organism: Homo sapiens
    Gene Names: Gene View for UBA3 UBE1C
    UniProtKB: Protein Feature View | Search PDB | Q8TBC4  
    Molecule: NEDD8
    Polymer: 3 Type: protein Length: 82
    Chains: I, J
    Organism: Homo sapiens
    Gene Name: Gene View for NEDD8
    UniProtKB: Protein Feature View | Search PDB | Q15843  
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Spodoptera frugiperda  
    Polymer: 2
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Spodoptera frugiperda  
    Polymer: 3
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Spodoptera frugiperda  
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    B39
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    B39 C21 H25 N5 O4 S
    [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden- 1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}- 2-hydroxycyclopentyl]methyl sulfamate
    B39:3GZN
    ZN
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    ZN Zn
    ZINC ION
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    B39
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    B39
    N/Ain BindingDB
    N/Ain BindingMoad
    IC50: 10 nM - data from PDBbind  
     
  •   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 and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Sintchak, M.D.

    Deposition:   2009-04-07
    Release:   2010-02-02
    Last Modified (REVDAT):   2012-03-21
     
  •   Revision History    Hide
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    2012-03-21
    Citation
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   3.00
    R-Value: 0.233 (obs.)
    R-Free: 0.287
    Space Group: I 2 2 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 135.03 α = 90.00 
    b = 228.71 β = 90.00 
    c = 229.31 γ = 90.00