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Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV.
Biology and Chemistry Report
3II6
  •   Structure Details   Hide

    Structure Keywords

    Keywords LIGASE/DNA BINDING PROTEIN
    Text XRCC4, DNA LIGASE IV, NHEJ, DNA REPAIR, BRCT, DNA damage, DNA recombination, Isopeptide bond, Nucleus, Phosphoprotein, ATP-binding, Cell cycle, Cell division, Disease mutation, DNA replication, Ligase, Magnesium, Metal-binding, Nucleotide-binding, SCID, LIGASE-DNA BINDING PROTEIN COMPLEX

    Polymeric Molecules

    Chain A,B,C,D
    Description DNA repair protein XRCC4 
    Fragment residues 1-203 
    Mutation A60E, I134T 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23424.7 
    Source Method genetically manipulated  
    Entity Name X-ray repair cross-complementing protein 4 
    Chain X,Y
    Description DNA ligase 4 
    Fragment C-Terminal tandem BRCT domains, residues 654-911 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 30221.6 
    Source Method genetically manipulated  
    Entity Name DNA ligase IV, Polydeoxyribonucleotide synthase [ATP] 4 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CL  CHLORIDE ION  Cl   35.45  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D XRCC4_HUMAN A8K3X4     
    X,Y DNLI4_HUMAN P49917     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    X Y  6.5.1.1      
     
  •   Gene Details   Hide

    Genetic Source

    Chain X,Y
    Common Name Human
    Scientific Name Homo sapiens  
    Gene lig4
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pPROEX


    Chain A,B,C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Gene xrcc4
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pACYC


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    5 5q14.2 7518     X-ray repair complementing defective repair in Chinese hamster cells 4 XRCC4    
    13 13q33-q34 3981     ligase IV, DNA, ATP-dependent LIG4    

    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
    rs142575170 LS-SNP   dbSNP   A 2 E - > K Coil 51% (Exposed) 5 82400742
    rs28383138 LS-SNP   dbSNP   A 12 S - > C Turn 20% (Intermediate) 5 82400773
    rs28383151 LS-SNP   dbSNP   A 56 A - > T Helix 2% (Buried) 5 82406873
    rs61762970 LS-SNP   dbSNP   A 75 L - > S Turn 14% (Intermediate) 5 82406931
    rs149355996 LS-SNP   dbSNP   A 87 N - > Y Beta Ladder 15% (Intermediate) 5 82406966
    rs144653114 LS-SNP   dbSNP   A 103 D - > N Bend 38% (Exposed) 5 82407014
    rs79561451 LS-SNP   dbSNP   A 110 S - > P Beta Ladder 28% (Intermediate) 5 82491601
    rs28360135 LS-SNP   dbSNP   A 134 I - > T Helix 11% (Intermediate) 5 82491674
    rs56334522 LS-SNP   dbSNP   A 137 N - > K Helix 16% (Intermediate) 5 82491684
    rs28360136 LS-SNP   dbSNP   A 142 E - > Q Helix 60% (Exposed) 5 82491697
    rs140143447 LS-SNP   dbSNP   A 179 R - > W Helix 14% (Intermediate) 5 82499423
    rs149774284 LS-SNP   dbSNP   X 654 K - > N Coil 107% (Exposed) 13 108861655
    rs139713386 LS-SNP   dbSNP   X 658 I - > M Turn 24% (Intermediate) 13 108861643
    rs2232641 LS-SNP   dbSNP   X 658 I - > V Turn 24% (Intermediate) 13 108861645
    rs143767581 LS-SNP   dbSNP   X 741 R - > H 3/10 Helix 40% (Exposed) 13 108861395
    rs138080550 LS-SNP   dbSNP   X 749 S - > P Helix 68% (Exposed) 13 108861372
    rs147410837 LS-SNP   dbSNP   X 756 R - > H Turn 58% (Exposed) 13 108861350
    rs141178992 LS-SNP   dbSNP   X 769 T - > A Coil 5% (Buried) 13 108861312
    rs200756045 LS-SNP   dbSNP   X 786 E - > K Bend 76% (Exposed) 13 108861261
    rs138936350 LS-SNP   dbSNP   X 797 A - > S Helix 8% (Buried) 13 108861228
    rs149457381 LS-SNP   dbSNP   X 800 E - > G Helix 2% (Buried) 13 108861218
    rs191975795 LS-SNP   dbSNP   X 808 S - > C Coil 24% (Intermediate) 13 108861194
    rs137899041 LS-SNP   dbSNP   X 809 P - > A 3/10 Helix 32% (Intermediate) 13 108861192
    rs145152896 LS-SNP   dbSNP   X 817 T - > A Beta Ladder 20% (Intermediate) 13 108861168
    rs141441003 LS-SNP   dbSNP   X 822 S - > L Coil 9% (Intermediate) 13 108861152
    rs146597721 LS-SNP   dbSNP   X 829 L - > R 3/10 Helix 63% (Exposed) 13 108861131
    rs199526538 LS-SNP   dbSNP   X 831 T - > I 3/10 Helix 20% (Intermediate) 13 108861125
    rs200369995 LS-SNP   dbSNP   X 840 I - > V Helix 7% (Buried) 13 108861099
    rs72660870 LS-SNP   dbSNP   X 842 A - > D Helix 16% (Intermediate) 13 108861092
    rs188422094 LS-SNP   dbSNP   X 850 A - > V Coil 7% (Buried) 13 108861068
    rs2232642 LS-SNP   dbSNP   X 857 A - > T Coil 43% (Exposed) 13 108861048
    rs201115578 LS-SNP   dbSNP   X 862 H - > Q Beta Ladder 7% (Buried) 13 108861031
    rs201176444 LS-SNP   dbSNP   X 862 H - > Y Beta Ladder 7% (Buried) 13 108861033
    rs183928755 LS-SNP   dbSNP   X 871 R - > H Turn 8% (Buried) 13 108861005
    rs201900772 LS-SNP   dbSNP   X 881 T - > S Turn 73% (Exposed) 13 108860976
    rs142374894 LS-SNP   dbSNP   X 886 F - > Y Coil 2% (Buried) 13 108860960
    rs148711190 LS-SNP   dbSNP   X 888 I - > F Beta Ladder 0% (Buried) 13 108860955