LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA
DOI:10.2210/pdb1m18/pdb   NDB ID: PD0328
1M18
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Structural Protein/dna
    Structure Weight: 201947.58
    Molecule: Palindromic 146 Base Pair DNA Fragment
    Polymer: 1 Type: dna Length: 146
    Chains: I, J
    Molecule: Histone H3.2
    Polymer: 2 Type: protein Length: 135
    Chains: A, E
    Organism: Xenopus laevis
    Gene Name: h3f3c
    UniProtKB: Protein Feature View | Search PDB | P02302  
    Molecule: Histone H4
    Polymer: 3 Type: protein Length: 102
    Chains: B, F
    Organism: Xenopus laevis
    UniProtKB: Protein Feature View | Search PDB | P62799  
    Molecule: Histone H2A.1
    Polymer: 4 Type: protein Length: 129
    Chains: C, G
    Organism: Xenopus laevis
    UniProtKB: Protein Feature View | Search PDB | P06897  
    Molecule: Histone H2B.1
    Polymer: 5 Type: protein Length: 125
    Chains: D, H
    Organism: Xenopus laevis
    UniProtKB: Protein Feature View | Search PDB | P02281  
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 2
    Scientific Name: Xenopus laevis   Taxonomy   Common Name: African clawed frog Expression System: Escherichia coli  
    Polymer: 3
    Scientific Name: Xenopus laevis   Taxonomy   Common Name: African clawed frog Expression System: Escherichia coli  
    Polymer: 4
    Scientific Name: Xenopus laevis   Taxonomy   Common Name: African clawed frog Expression System: Escherichia coli  
    Polymer: 5
    Scientific Name: Xenopus laevis   Taxonomy   Common Name: African clawed frog Expression System: Escherichia coli  
     
  •   Related PDB Entries Hide
    Identifier Details
    1AOI   Original nucleosome core particle structure. 
    1M19   Nucleosome core particle structure with related ligand, Polyamide 2 bound. 
    1M1A   Nucleosome core particle structure with related ligand, Polyamide 3 bound. 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    1SZ
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    1SZ C58 H71 N21 O10
    N-[5-[[4-[[5-[[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]- 3-oxidanylidene-propyl]carbamoyl]-1-methyl- pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3- yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]- 1-methyl-pyrrol-3-yl]amino]-4-oxidanylidene- butyl]carbamoyl]-1-methyl-pyrrol-3-yl]-1- methyl-4-[[1-methyl-4-[(1-methylimidazol- 2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]imidazole- 2-carboxamide
    MN
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    MN Mn
    MANGANESE (II) ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:PD0328
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors
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  •   Deposition Summary Hide
    Authors:   Suto, R.K.,  Edayathumangalam, R.S.,  White, C.L.,  Melander, C.,  Gottesfeld, J.M.,  Dervan, P.B.,  Luger, K.

    Deposition:   2002-06-18
    Release:   2003-02-18
    Last Modified (REVDAT):   2013-07-17
     
  •   Revision History    Hide
    Mouse over text for details
    2013-07-17
    Non-polymer description
    2013-07-17
    Sequence database correspondence
    2011-07-13
    Version format compliance
    2011-07-13
    Non-polymer description
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
    N/A
    Resolution[Å]:   2.45
    R-Value: 0.222 (work)
    R-Free: 0.257
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 106.84 α = 90.00 
    b = 109.63 β = 90.00 
    c = 183.17 γ = 90.00