HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine as a target base (GPGC:GMGC) and SAH
DOI:10.2210/pdb2c7r/pdb   NDB ID: PD0936
2C7R
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 45880.67
    Molecule: MODIFICATION METHYLASE HHAI
    Polymer: 1 Type: protein Length: 327
    Chains: A
    EC#: 2.1.1.37   
    Mutation: YES
    Organism: Haemophilus haemolyticus
    Gene Name: hhaIM
    UniProtKB: Protein Feature View | Search PDB | P05102  
    Molecule: 5'-D(*G*GP*AP*TP*GP*(5CM)*GP*CP*TP*GP*AP*C)-3'
    Polymer: 2 Type: dna Length: 12
    Chains: C
    Organism: synthetic construct
    Molecule: 5'-D(*G*TP*CP*AP*GP*(2PR)*GP*CP*AP*TP*CP*C)-3'
    Polymer: 3 Type: dna Length: 12
    Chains: D
    Organism: synthetic construct
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Haemophilus haemolyticus   Taxonomy   Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct (synthetic construct)   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct (synthetic construct)   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    10MH   TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND HEMIMETHYLATED DEOXYRIBONUCLEIC ACID CONTAINING 5,6-DIHYDRO-5-AZACYTOSINE AT THE TARGET 
    1FJX   STRUCTURE OF TERNARY COMPLEX OF HHAI METHYLTRANSFERASEMUTANT (T250G) IN COMPLEX WITH DNA AND ADOHCY 
    1HMY   HHAI DEOXYRIBONUCLEIC ACID (CYTOSINE-C5-)- METHYLTRANSFERASE COMPLEX WITH S-ADENOSYL-L- METHIONINE 
    1M0E   ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS ACOVALENT COMPLEX WITH DNA METHYLTRANSFERASE 
    1MHT   COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DEOXYRIBONUCLEIC ACID AND S- ADENOSYL-L-HOMOCYSTEINE 
    1SKM   HHAI METHYLTRANSFERASE IN COMPLEX WITH DNA CONTAINING ANABASIC SOUTH CARBOCYCLIC SUGAR AT ITS TARGET SITE 
    1SVU   STRUCTURE OF THE Q237W MUTANT OF HHAI DNAMETHYLTRANSFERASE: AN INSIGHT INTO PROTEIN- PROTEININTERACTIONS 
    2C7O   HHAI DNA METHYLTRANSFERASE COMPLEX WITH 13MER OLIGONUCLEOTIDE CONTAINING 2-AMINOPURINE ADJACENT TO THE TARGET BASE (PCGC:GMGC) AND SAH 
    2C7P   HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING 2-AMINOPURINE OPPOSITE TO THE TARGET BASE (GCGC:GMPC) AND SAH 
    2C7Q   HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING 2-AMINOPURINE OUTSIDE THE RECOGNITION SEQUENCE (PAIRED WITH G) AND SAH 
    2HMY   BINARY COMPLEX OF HHAI METHYLTRANSFERASE WITH ADOMET FORMED IN THE PRESENCE OF A SHORT NONPSECIFIC DEOXYRIBONUCLEIC ACID OLIGONUCLEOTIDE 
    3MHT   TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH UNMODIFIED DEOXYRIBONUCLEIC ACID AND ADOHCY 
    4MHT   TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH NATIVE DEOXYRIBONUCLEIC ACID AND ADOHCY 
    5MHT   TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH HEMIMETHYLATED DEOXYRIBONUCLEIC ACID AND ADOHCY 
    6MHT   TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND DEOXYRIBONUCLEIC ACID CONTAINING 4'-THIO-2'DEOXYCYTIDINE AT THE TARGET 
    7MHT   CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/ DEOXYRIBONUCLEIC ACID COMPLEX 
    8MHT   CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/ DEOXYRIBONUCLEIC ACID COMPLEX 
    9MHT   CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/ DEOXYRIBONUCLEIC ACID COMPLEX 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    GOL
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    GOL C3 H8 O3
    GLYCEROL
    SAH
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    SAH C14 H20 N6 O5 S
    S-ADENOSYL-L-HOMOCYSTEINE
    SAH:2C7R
    SO4
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    SO4 O4 S
    SULFATE ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    5CM
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    5CM C10 H16 N3 O7 P DC dnaLinking
    2PR
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    2PR C10 H14 N5 O6 P DG dnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:PD0936
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PQS (software)
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  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Daujotyte, D.,  Grazulis, S.

    Deposition:   2005-11-27
    Release:   2005-12-14
    Last Modified (REVDAT):   2014-01-29
     
  •   Revision History    Hide
    Mouse over text for details
    2014-01-29
    Version format compliance
    2014-01-29
    Function and keywords
    2014-01-29
    Source and taxonomy
    2014-01-29
    Atom nomenclature
    2014-01-29
    Biological assembly
    2014-01-29
    Linkage
    2014-01-29
    Polymer description
    2014-01-29
    Refinement description
    2014-01-29
    Other
    2014-01-29
    Non-polymer description
    2014-01-29
    Geometry validation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
    N/A
    Resolution[Å]:   1.90
    R-Value: 0.199 (obs.)
    R-Free: 0.217
    Space Group: H 3 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 95.62 α = 90.00 
    b = 95.62 β = 90.00 
    c = 315.76 γ = 120.00