PDB entry 2zkd

View 2zkd on RCSB PDB site
Description: Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA
Class: ligase
Keywords: Protein-DNA complex, Cell cycle, Developmental protein, DNA damage, DNA repair, DNA-binding, Ligase, Metal-binding, Nucleus, Phosphoprotein, Transcription, Transcription regulation, Ubl conjugation, Ubl conjugation pathway, Zinc, Zinc-finger
Deposited on 2008-03-19, released 2008-09-09
The last revision prior to the SCOP 1.75 freeze date was dated 2008-10-14, with a file datestamp of 2008-10-10.
Experiment type: XRAY
Resolution: 1.6 Å
R-factor: 0.156
AEROSPACI score: 0.73 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: E3 ubiquitin-protein ligase UHRF1
    Species: Mus musculus [TaxId:10090]
    Gene: Uhrf1, Np95
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8VDF2 (0-209)
      • engineered (0)
    Domains in SCOP 1.75: d2zkda1
  • Chain 'B':
    Compound: E3 ubiquitin-protein ligase UHRF1
    Species: Mus musculus [TaxId:10090]
    Gene: Uhrf1, Np95
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8VDF2 (0-End)
      • engineered (0)
    Domains in SCOP 1.75: d2zkdb1
  • Chain 'C':
    Compound: DNA (5'-d(*dcp*dtp*dap*dcp*dcp*dgp*dgp*dap*dtp*dtp*dgp*dc)-3')
    Species: synthetic, synthetic
  • Chain 'D':
    Compound: DNA (5'-d(*dgp*dcp*dap*dap*dtp*dcp*(5cm)p*dgp*dgp*dtp*dap*dg)-3')
    Species: synthetic, synthetic
  • Chain 'E':
    Compound: DNA (5'-d(*dcp*dtp*dap*dcp*dcp*dgp*dgp*dap*dtp*dtp*dgp*dc)-3')
    Species: synthetic, synthetic
  • Chain 'F':
    Compound: DNA (5'-d(*dgp*dcp*dap*dap*dtp*dcp*(5cm)p*dgp*dgp*dtp*dap*dg)-3')
    Species: synthetic, synthetic
  • Heterogens: ACT, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2zkdA (A:)
    sgmacvgrttectivpanhfgpipgvpvgtmwrfrvqvsesgvhrphvagihgrsndgay
    slvlaggyeddvdngnyftytgsggrdlsgnkrtagqssdqkltnnnralalnchspine
    kgaeaedwrqgkpvrvvrnmkggkhskyapaegnrydgiykvvkywpergksgflvwryl
    lrrddtepepwtregkdrtrqlgltmqype
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2zkdB (B:)
    sgmacvgrttectivpanhfgpipgvpvgtmwrfrvqvsesgvhrphvagihgrsndgay
    slvlaggyeddvdngnyftytgsggrdlsgnkrtagqssdqkltnnnralalnchspine
    kgaeaedwrqgkpvrvvrnmkggkhskyapaegnrydgiykvvkywpergksgflvwryl
    lrrddtepepwtregkdrtrqlgltmqype
    

    Sequence, based on observed residues (ATOM records): (download)
    >2zkdB (B:)
    sgmacvgrttectivpanhfgpipgvpvgtmwrfrvqvsesgvhrphvagihgrsndgay
    slvlaggyeddvdngnyftytgsggrdlsgnkrtagqssdqkltnnnralalnchspine
    kgaeaedwrqgkpvrvvrnmkggkhskyapaegnrydgiykvvkywpergksgflvwryl
    lrrddtepepwtregkdrtrqlgltmqyp
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.