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An Information Portal to 105025 Biological Macromolecular Structures

Crystal structure of human DNMT1(646-1600) in complex with DNA
Biology and Chemistry Report
3PTA
  •   Structure Details   Hide

    Structure Keywords

    Keywords Transferase/DNA
    Text DNMT1, Maintenance DNA methylation, Transferase-DNA complex

    Polymeric Molecules

    Chain A
    Description DNA (cytosine-5)-methyltransferase 1 
    Fragment UNP residues 646-1600 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 108061.0 
    Source Method genetically manipulated  
    Entity Name Dnmt1, CXXC-type zinc finger protein 9, DNA methyltransferase HsaI, DNA MTase HsaI, M.HsaI, MCMT 
    Chain B
    Description DNA (5'-D(*TP*CP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*CP*CP*GP*CP*AP*GP*G)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 5782.8 
    Source Method synthetic  
    Chain C
    Description DNA (5'-D(*CP*CP*TP*GP*CP*GP*GP*AP*GP*GP*CP*TP*CP*AP*CP*GP*GP*GP*A)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 5871.8 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    SAH  S-ADENOSYL-L-HOMOCYSTEINE  C14 H20 N6 O5 S   384.41  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A DNMT1_HUMAN A0AV63     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    2.1.1.37      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6306   DNA Methylation  The Covalent Transfer of a Methyl Group to Either N 6 of Adenine or C 5 or N 4 of Cytosine. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3682   Chromatin Binding  Interacting Selectively and Non Covalently with Chromatin the Network of Fibers of DNA Protein and Sometimes RNA That Make Up the Chromosomes of the Eukaryotic Nucleus During Interphase. 
    8168   Methyltransferase Activity  Catalysis of the Transfer of a Methyl Group to an Acceptor Molecule. 
    8270   Zinc Ion Binding  Interacting Selectively and Non Covalently with Zinc (zn) Ions. 


    Protein Analyses

    Measured Binding Affinities   

     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene dnmt1, aim, cxxc9, dnmt
    Host Scientific Name Escherichia coli  
    Host Strain C41(de3)


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    19 19p13.2 1786     DNA (cytosine-5-)-methyltransferase 1 DNMT1    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs146467216 LS-SNP   dbSNP   A 647 A - > T Coil 130% (Exposed) 19 10265001
    rs142562681 LS-SNP   dbSNP   A 756 T - > N Beta Ladder 57% (Exposed) 19 10260595
    rs113497353 LS-SNP   dbSNP   A 774 L - > P Coil 44% (Exposed) 19 10260541
    rs148987580 LS-SNP   dbSNP   A 780 T - > M Beta Ladder 11% (Intermediate) 19 10260328
    rs183555527 LS-SNP   dbSNP   A 806 G - > R Turn 12% (Intermediate) 19 10260251
    rs140993011 LS-SNP   dbSNP   A 808 T - > M Turn 18% (Intermediate) 19 10260244
    rs62621087 LS-SNP   dbSNP   A 860 G - > R Coil 119% (Exposed) 19 10259654
    rs201213597 LS-SNP   dbSNP   A 882 T - > I Coil 37% (Exposed) 19 10259587
    rs150863675 LS-SNP   dbSNP   A 894 V - > L Helix 32% (Intermediate) 19 10257193
    rs199827346 LS-SNP   dbSNP   A 1017 R - > Q Beta Ladder 27% (Intermediate) 19 10254460
    rs144533539 LS-SNP   dbSNP   A 1017 R - > W Beta Ladder 27% (Intermediate) 19 10254461
    rs187394074 LS-SNP   dbSNP   A 1050 V - > M Beta Ladder 53% (Exposed) 19 10252817
    rs140852137 LS-SNP   dbSNP   A 1059 R - > C Beta Ladder 31% (Intermediate) 19 10252790
    rs150331990 LS-SNP   dbSNP   A 1102 H - > R 3/10 Helix 70% (Exposed) 19 10251822
    rs200950656 LS-SNP   dbSNP   A 1104 R - > C Bend 40% (Exposed) 19 10251817
    rs151305495 LS-SNP   dbSNP   A 1157 Q - > H Helix 41% (Exposed) 19 10251461
    rs201497993 LS-SNP   dbSNP   A 1203 T - > N Bend 78% (Exposed) 19 10250872
    rs142648642 LS-SNP   dbSNP   A 1204 T - > I Beta 43% (Exposed) 19 10250869
    rs200312526 LS-SNP   dbSNP   A 1289 R - > C Helix 23% (Intermediate) 19 10250387
    rs141791913 LS-SNP   dbSNP   A 1338 A - > V 3/10 Helix 5% (Buried) 19 10249169
    rs201167482 LS-SNP   dbSNP   A 1354 I - > L Coil 12% (Intermediate) 19 10249122
    rs139918621 LS-SNP   dbSNP   A 1426 R - > W Helix 60% (Exposed) 19 10247926
    rs142647321 LS-SNP   dbSNP   A 1460 H - > Q Coil 51% (Exposed) 19 10247822
    rs147984942 LS-SNP   dbSNP   A 1466 R - > C Coil 51% (Exposed) 19 10247806