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Crystal structure of XIAP BIR3 domain in complex with a Smac-mimetic compound
3EYL
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ligase
    Structure Weight: 29387.68
    Molecule: Baculoviral IAP repeat-containing protein 4
    Polymer: 1 Type: protein Length: 122
    Chains: A, B
    EC#: 6.3.2   
    Fragment: UNP residues 241-356
    Organism: Homo sapiens
    Gene Names: Gene View for XIAP API3 BIRC4 IAP3
    UniProtKB: Protein Feature View | Search PDB | P98170  
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Escherichia coli  
     
  •   Related PDB Entries Hide
    Identifier Details
    1g73  XIAP/BIR3 domain in complex with Smac N-terminal sequence AVPI 
    3clx  XIAP/BIR3 domain in complex with Smac mimetic, Smac005 
    3cm2  XIAP/BIR3 domain in complex with Smac mimetic, Smac010 
    3cm7  XIAP/BIR3 domain in complex with Smac mimetic, Smac005 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    SMK
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    SMK C29 H39 N5 O3
    (3S,6S,7R,9aS)-6-{[(2S)-2-aminobutanoyl]amino}- 7-(2-aminoethyl)-N-(diphenylmethyl)-5-oxooctahydro- 1H-pyrrolo[1,2-a]azepine-3-carboxamide
    SMK:3EYL
    ZN
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    ZN Zn
    ZINC ION
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    SMK
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    SMK
    IC50: 86 - 250 nM (100) - data from BindingDB  
    Ki: 220 nM (100) - 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).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Cossu, F.,  Milani, M.,  Mastrangelo, E.,  Bolognesi, M.

    Deposition:   2008-10-21
    Release:   2008-11-25
    Last Modified (REVDAT):   2011-07-13
     
  •   Revision History    Hide
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    2011-07-13
    Version format compliance
    2011-07-13
    Flag residual B-value
    2011-07-13
    Refinement description
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   3.00
    R-Value: 0.191 (obs.)
    R-Free: 0.239
    Space Group: I 41 3 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 170.42 α = 90.00 
    b = 170.42 β = 90.00 
    c = 170.42 γ = 90.00