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Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium
DOI:10.2210/pdb3l2r/pdb   NDB ID: NA0397
3L2R
Primary Citation
 
 
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  •   Molecular Description Hide
    Classification: Recombination/dna
    Structure Weight: 100535.21
    Molecule: Integrase
    Polymer: 1 Type: protein Length: 395
    Chains: A, B
    Organism Human spumaretrovirus
    Gene Name pol
    UniProtKB:   Protein Feature View | Search PDB | P14350  
    Molecule: 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*TP*GP*TP*A)-3'
    Polymer: 2 Type: dna Length: 19
    Chains: C
    Details: 19 nucleotide preprocessed PFV donor DNA
    Molecule: 5'-D(*TP*AP*CP*AP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3'
    Polymer: 3 Type: dna Length: 17
    Chains: D
    Details: 17 nucleotide preprocessed PFV donor DNA
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Human spumaretrovirus   Taxonomy   Common Name: Sfvcpz(hu) Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3DLR  Catalytic core domain of PFV IN 
    3L2Q  the same protein in apo form 
    3L2S  the same protein in complex with manganese 
    3L2T  the same protein in complex with magnesium and MK0518 (Raltegravir) 
    3L2U  the same protein in complex with magnesium and GS9137 (Elvitegravir) 
    3L2V  the same protein in complex with manganese and MK0518 (Raltegravir) 
    3L2W  the same protein in complex with manganese and GS9137 (Elvitegravir) 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name Interactions
    GOL
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    Download      		GOL C3 H8 O3
    GLYCEROL
    MG
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    Download      		MG Mg
    MAGNESIUM ION
    NH4
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    Download      		NH4 H4 N
    AMMONIUM ION
    ZN
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    Download      		ZN Zn
    ZINC ION
     
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  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA0397
     
 
Data in orange boxes are gathered from external resources (when available).
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  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Hare, S.,  Gupta, S.S.,  Cherepanov, P.

    Deposition:   2009-12-15
    Release:   2010-02-09
    Last Modified (REVDAT):   2010-03-16
     
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    2011-07-13
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  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.88
    R-Value: 0.203 (obs.)
    R-Free: 0.222
    Space Group: P 41 21 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 158.48 α = 90.00 
    b = 158.48 β = 90.00 
    c = 124.19 γ = 90.00