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Human Aprataxin (Aptx) bound to DNA, AMP, and Zn - product complex
Biology and Chemistry Report
4NDH
  •   Structure Details   Hide

    Structure Keywords

    Keywords DNA BINDING PROTEIN/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-DNA complex

    Polymeric Molecules

    Chain A,B
    Description Aprataxin 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 21259.9 
    Source Method genetically manipulated  
    Entity Name Forkhead-associated domain histidine triad-like protein, FHA-HIT 
    Chain D,E,G,H
    Description 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 3044.0 
    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 
    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      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6281   DNA Repair  The Process of Restoring DNA After Damage. Genomes Are Subject to Damage by Chemical and Physical Agents in the Environment (e.g. Uv and Ionizing Radiations Chemical Mutagens Fungal and Bacterial Toxins Etc.) and by Free Radicals or Alkylating Agents Endogenously Generated in Metabolism. DNA Is Also Damaged Because of Errors During Its Replication. a Variety of Different DNA Repair Pathways Have Been Reported That Include Direct Reversal Base Excision Repair Nucleotide Excision Repair Photoreactivation Bypass Double Strand Break Repair Pathway and Mismatch Repair Pathway. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    33699   DNA 5' Adenosine Monophosphate Hydrolase Activity  Catalysis of the Reaction: 5' AMP DNA + H2o = AMP + Dna; Nucleophilic Release of a Covalently Linked Adenylate Residue From a DNA Strand Leaving a 5' Phosphate Terminus. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   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 25% (Intermediate) 9 32984803
    rs150886026 LS-SNP   dbSNP   A 199 R - > H Bend 25% (Intermediate) 9 32984803
    rs150886026 LS-SNP   dbSNP   A 199 R - > H Bend 25% (Intermediate) 9 32984803
    rs121908133 LS-SNP   dbSNP   A 201 H - > R Beta Ladder 4% (Buried) 9 32984797 NULL
    rs121908133 LS-SNP   dbSNP   A 201 H - > R Beta Ladder 4% (Buried) 9 32984797 NULL
    rs121908133 LS-SNP   dbSNP   A 201 H - > R Beta Ladder 4% (Buried) 9 32984797 NULL
    rs121908131 LS-SNP   dbSNP   A 206 P - > L Beta Ladder 0% (Buried) 9 32984782
    rs121908131 LS-SNP   dbSNP   A 206 P - > L Beta Ladder 0% (Buried) 9 32984782
    rs121908131 LS-SNP   dbSNP   A 206 P - > L Beta Ladder 0% (Buried) 9 32984782
    rs142133683 LS-SNP   dbSNP   A 247 R - > Q Beta Ladder 19% (Intermediate) 9 32984659
    rs142133683 LS-SNP   dbSNP   A 247 R - > Q Beta Ladder 19% (Intermediate) 9 32984659
    rs142133683 LS-SNP   dbSNP   A 247 R - > Q Beta Ladder 19% (Intermediate) 9 32984659
    rs141195622 LS-SNP   dbSNP   A 248 L - > M Beta Ladder 9% (Intermediate) 9 32984657
    rs141195622 LS-SNP   dbSNP   A 248 L - > M Beta Ladder 9% (Intermediate) 9 32984657
    rs141195622 LS-SNP   dbSNP   A 248 L - > M Beta Ladder 9% (Intermediate) 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 12% (Intermediate) 9 32974516
    rs144893610 LS-SNP   dbSNP   A 272 C - > R Turn 12% (Intermediate) 9 32974516
    rs144893610 LS-SNP   dbSNP   A 272 C - > R Turn 12% (Intermediate) 9 32974516
    rs149867156 LS-SNP   dbSNP   A 295 E - > K Helix 55% (Exposed) 9 32973642
    rs149867156 LS-SNP   dbSNP   A 295 E - > K Helix 55% (Exposed) 9 32973642
    rs149867156 LS-SNP   dbSNP   A 295 E - > K Helix 55% (Exposed) 9 32973642
    rs12001066 LS-SNP   dbSNP   A 310 P - > L Helix 51% (Exposed) 9 32973596
    rs12001066 LS-SNP   dbSNP   A 310 P - > L Helix 51% (Exposed) 9 32973596
    rs12001066 LS-SNP   dbSNP   A 310 P - > L Helix 51% (Exposed) 9 32973596
    rs141493373 LS-SNP   dbSNP   A 324 Q - > L Coil 47% (Exposed) 9 32973554 NULL
    rs141493373 LS-SNP   dbSNP   A 324 Q - > L Coil 47% (Exposed) 9 32973554 NULL
    rs141493373 LS-SNP   dbSNP   A 324 Q - > L Coil 47% (Exposed) 9 32973554 NULL
    rs200782765 LS-SNP   dbSNP   A 339 H - > R 3/10 Helix 41% (Exposed) 9 32973509 NULL
    rs200782765 LS-SNP   dbSNP   A 339 H - > R 3/10 Helix 41% (Exposed) 9 32973509 NULL
    rs200782765 LS-SNP   dbSNP   A 339 H - > R 3/10 Helix 41% (Exposed) 9 32973509 NULL