PDB entry 3ez5

View 3ez5 on RCSB PDB site
Description: Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and zinc (closed form).
Class: transferase/DNA
Keywords: protein-DNA complex, TRANSFERASE-DNA COMPLEX
Deposited on 2008-10-22, released 2009-11-10
The last revision prior to the SCOPe 2.07 freeze date was dated 2010-03-02, with a file datestamp of 2010-02-26.
Experiment type: XRAY
Resolution: 1.9 Å
R-factor: 0.212
AEROSPACI score: 0.45 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA polymerase I
    Species: Bacillus stearothermophilus
    Gene: polA
    Database cross-references and differences (RAF-indexed):
    • PDB 3EZ5 (0-579)
      • engineered (413)
    Domains in SCOPe 2.07: d3ez5a1, d3ez5a2
  • Chain 'B':
    Compound: 5'-d(*dcp*dcp*dtp*dgp*dap*dcp*dtp*dcp*dg)-3'
  • Chain 'C':
    Compound: 5'-d(*dap*dtp*dtp*dcp*dgp*dap*dgp*dtp*dcp*dap*dgp*dg)-3'
  • Chain 'D':
    Compound: DNA polymerase I
    Species: Bacillus stearothermophilus
    Gene: polA
    Database cross-references and differences (RAF-indexed):
    • PDB 3EZ5 (Start-579)
      • engineered (413)
    Domains in SCOPe 2.07: d3ez5d1, d3ez5d2
  • Chain 'E':
    Compound: 5'-d(*dcp*dcp*dtp*dgp*dap*dcp*dtp*dcp*dg)-3'
  • Chain 'F':
    Compound: 5'-d(*dap*dtp*dtp*dcp*dgp*dap*dgp*dtp*dcp*dap*dgp*dg)-3'
  • Heterogens: DAD, ZN, SUC, SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3ez5A (A:)
    kkmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrfflrpetaladpq
    fvawlgdetkkksmfdskraavalkwkgielcgvsfdlllaaylldpaqgvddvaaaakm
    kqyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpfldelrrneqdrllve
    leqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagqefninspkqlgv
    ilfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgklqstyiegllkvvr
    patkkvhtifnqaltqtgrlsstepnlqnipirleegrkirqafvpsesdwlifaadysq
    ielrvlahiaeddnlmeafrrdldihtktamdifqvsedevtpnmrrqakavnygivygi
    sdyglaqnlnisrkeaaefieryfesfpgvkrymenivqeakqkgyvttllhrrrylpdi
    tsrnfnvrsfaermamntpiqgsaadiikkamidlnarlkeerlqahlllqvhdelilea
    pkeemerlcrlvpevmeqavtlrvplkvdyhygstwydak
    

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3ez5D (D:)
    kkmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrfflrpetaladpq
    fvawlgdetkkksmfdskraavalkwkgielcgvsfdlllaaylldpaqgvddvaaaakm
    kqyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpfldelrrneqdrllve
    leqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagqefninspkqlgv
    ilfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgklqstyiegllkvvr
    patkkvhtifnqaltqtgrlsstepnlqnipirleegrkirqafvpsesdwlifaadysq
    ielrvlahiaeddnlmeafrrdldihtktamdifqvsedevtpnmrrqakavnygivygi
    sdyglaqnlnisrkeaaefieryfesfpgvkrymenivqeakqkgyvttllhrrrylpdi
    tsrnfnvrsfaermamntpiqgsaadiikkamidlnarlkeerlqahlllqvhdelilea
    pkeemerlcrlvpevmeqavtlrvplkvdyhygstwydak
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ez5D (D:)
    kmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrfflrpetaladpqf
    vawlgdetkkksmfdskraavalkwkgielcgvsfdlllaaylldpaqgvddvaaaakmk
    qyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpfldelrrneqdrllvel
    eqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagqefninspkqlgvi
    lfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgklqstyiegllkvvrp
    atkkvhtifnqaltqtgrlsstepnlqnipirleegrkirqafvpsesdwlifaadysqi
    elrvlahiaeddnlmeafrrdldihtktamdifqvsedevtpnmrrqakavnygivygis
    dyglaqnlnisrkeaaefieryfesfpgvkrymenivqeakqkgyvttllhrrrylpdit
    srnfnvrsfaermamntpiqgsaadiikkamidlnarlkeerlqahlllqvhdelileap
    keemerlcrlvpevmeqavtlrvplkvdyhygstwydak
    

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.