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Human Aprataxin (Aptx) AOA1 variant K197Q bound to RNA-DNA, AMP, and Zn - product complex
Biology and Chemistry Report
4NDI
  •   Structure Details   Hide

    Structure Keywords

    Keywords DNA BINDING PROTEIN/RNA/DNA
    Text protein-DNA complex, DNA repair, 5'-DNA end processing, Histidine Triad domain, HIT domain, Zinc finger, 5'-DNA end recognition, DNA BINDING PROTEIN-RNA-DNA complex

    Polymeric Molecules

    Chain A,B
    Description Aprataxin 
    Mutation K197Q 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 21258.9 
    Source Method genetically manipulated  
    Entity Name Forkhead-associated domain histidine triad-like protein, FHA-HIT 
    Chain D,G
    Description 5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide/polyribonucleotide hybrid 
    Formula Weight 3066.0 
    Source Method synthetic  
    Chain E,H
    Description 5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 3037.1 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    AMP  ADENOSINE MONOPHOSPHATE  C10 H14 N5 O7 P   347.22  View 
    BME  BETA-MERCAPTOETHANOL  C2 H6 O S   78.13  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    POTASSIUM ION  K   39.10  View 
    NA  SODIUM ION  Na   22.99  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B APTX_HUMAN A8MTN4     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  3      
     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene aptx, axa1
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET15b


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    9 9p13.3 54840     aprataxin APTX    

    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
    rs150886026 LS-SNP   dbSNP   A 199 R - > H Bend 46% (Exposed) 9 32984803
    rs150886026 LS-SNP   dbSNP   A 199 R - > H Bend 46% (Exposed) 9 32984803
    rs150886026 LS-SNP   dbSNP   A 199 R - > H Bend 46% (Exposed) 9 32984803
    rs121908133 LS-SNP   dbSNP   A 201 H - > R Beta Ladder 5% (Buried) 9 32984797 NULL
    rs121908133 LS-SNP   dbSNP   A 201 H - > R Beta Ladder 5% (Buried) 9 32984797 NULL
    rs121908133 LS-SNP   dbSNP   A 201 H - > R Beta Ladder 5% (Buried) 9 32984797 NULL
    rs121908131 LS-SNP   dbSNP   A 206 P - > L Beta Ladder 1% (Buried) 9 32984782
    rs121908131 LS-SNP   dbSNP   A 206 P - > L Beta Ladder 1% (Buried) 9 32984782
    rs121908131 LS-SNP   dbSNP   A 206 P - > L Beta Ladder 1% (Buried) 9 32984782
    rs142133683 LS-SNP   dbSNP   A 247 R - > Q Beta Ladder 20% (Intermediate) 9 32984659
    rs142133683 LS-SNP   dbSNP   A 247 R - > Q Beta Ladder 20% (Intermediate) 9 32984659
    rs142133683 LS-SNP   dbSNP   A 247 R - > Q Beta Ladder 20% (Intermediate) 9 32984659
    rs141195622 LS-SNP   dbSNP   A 248 L - > M Beta Ladder 8% (Buried) 9 32984657
    rs141195622 LS-SNP   dbSNP   A 248 L - > M Beta Ladder 8% (Buried) 9 32984657
    rs141195622 LS-SNP   dbSNP   A 248 L - > M Beta Ladder 8% (Buried) 9 32984657
    rs121908132 LS-SNP   dbSNP   A 263 V - > G Beta Ladder 1% (Buried) 9 32974542
    rs121908132 LS-SNP   dbSNP   A 263 V - > G Beta Ladder 1% (Buried) 9 32974542
    rs121908132 LS-SNP   dbSNP   A 263 V - > G Beta Ladder 1% (Buried) 9 32974542
    rs144893610 LS-SNP   dbSNP   A 272 C - > R Turn 23% (Intermediate) 9 32974516 NULL
    rs144893610 LS-SNP   dbSNP   A 272 C - > R Turn 23% (Intermediate) 9 32974516 NULL
    rs144893610 LS-SNP   dbSNP   A 272 C - > R Turn 23% (Intermediate) 9 32974516 NULL
    rs149867156 LS-SNP   dbSNP   A 295 E - > K Helix 54% (Exposed) 9 32973642
    rs149867156 LS-SNP   dbSNP   A 295 E - > K Helix 54% (Exposed) 9 32973642
    rs149867156 LS-SNP   dbSNP   A 295 E - > K Helix 54% (Exposed) 9 32973642
    rs12001066 LS-SNP   dbSNP   A 310 P - > L Helix 46% (Exposed) 9 32973596
    rs12001066 LS-SNP   dbSNP   A 310 P - > L Helix 46% (Exposed) 9 32973596
    rs12001066 LS-SNP   dbSNP   A 310 P - > L Helix 46% (Exposed) 9 32973596
    rs141493373 LS-SNP   dbSNP   A 324 Q - > L Coil 48% (Exposed) 9 32973554 NULL
    rs141493373 LS-SNP   dbSNP   A 324 Q - > L Coil 48% (Exposed) 9 32973554 NULL
    rs141493373 LS-SNP   dbSNP   A 324 Q - > L Coil 48% (Exposed) 9 32973554 NULL
    rs200782765 LS-SNP   dbSNP   A 339 H - > R 3/10 Helix 34% (Intermediate) 9 32973509 NULL
    rs200782765 LS-SNP   dbSNP   A 339 H - > R 3/10 Helix 34% (Intermediate) 9 32973509 NULL
    rs200782765 LS-SNP   dbSNP   A 339 H - > R 3/10 Helix 34% (Intermediate) 9 32973509 NULL