PDB entry 3px4

View 3px4 on RCSB PDB site
Description: Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (wobble) in Ajar Conformation
Class: transferase/DNA
Keywords: DNA Polymerase I, protein-DNA complex, TRANSFERASE-DNA complex, Cytosine-Adenine, closed conformation
Deposited on 2010-12-09, released 2011-10-19
The last revision prior to the SCOPe 2.05 freeze date was dated 2011-11-09, with a file datestamp of 2011-11-04.
Experiment type: XRAY
Resolution: 1.58 Å
R-factor: 0.212
AEROSPACI score: 0.57 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA polymerase I
    Species: Geobacillus kaustophilus [TaxId:1462]
    Gene: polA, GK2730
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5KWC1 (Start-591)
      • engineered mutation (313)
      • engineered mutation (425)
      • see remark 999 (538)
    Domains in SCOPe 2.05: d3px4a1, d3px4a2
  • Chain 'B':
    Compound: DNA (5'-d(*cp*cp*tp*gp*ap*cp*tp*cp*(doc))-3')
  • Chain 'C':
    Compound: DNA (5'-d(*cp*ap*tp*ap*gp*gp*ap*gp*tp*cp*ap*gp*g)-3')
  • Chain 'D':
    Compound: DNA polymerase I
    Species: Geobacillus kaustophilus [TaxId:1462]
    Gene: polA, GK2730
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5KWC1 (Start-591)
      • engineered mutation (313)
      • engineered mutation (425)
      • see remark 999 (538)
    Domains in SCOPe 2.05: d3px4d1, d3px4d2
  • Chain 'E':
    Compound: DNA (5'-d(*cp*cp*tp*gp*ap*cp*tp*cp*(doc))-3')
  • Chain 'F':
    Compound: DNA (5'-d(*cp*ap*tp*ap*gp*gp*ap*gp*tp*cp*ap*gp*g)-3')
  • Heterogens: DCT, MG, SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3px4A (A:)
mespsseeekplakmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrf
flrpetaladpqfvawlgdetkkksmfdskraavalkwkgielcgvsfdlllaaylldpa
qgvddvaaaakmkqyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpflde
lrrneqdrllveleqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagq
efninspkqlgvilfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgklq
styiegllkvvrpatkkvhtifnqaltqtgrlsstepnlqnipirleegrkirqafvpse
sdwlifaadysqielrvlahiaeddnlmeafrrdldihtktamdifqvsedevtpnmrrq
akavnygivygisdyglaqnlnisrkeaaefieryfesfpgvkrymenivqeakqkgyvt
tllhrrrylpditsrnfnvrsfaermamntpiqgsaadiikkamidlnarlkeerlqahl
llqvhdelileapkeemerlcrlvpevmeqavtlrvplkvdyhygstwydak

    Sequence, based on observed residues (ATOM records): (download) 
    >3px4A (A:)
kmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrfflrpetaladpqf
vawlgdetkkksmfdskraavalkwkgielcgvsfdlllaaylldpaqgvddvaaaakmk
qyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpfldelrrneqdrllvel
eqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagqefninspkqlgvi
lfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgklqstyiegllkvvrp
atkkvhtifnqaltqtgrlsstepnlqnipirleegrkirqafvpsesdwlifaadysqi
elrvlahiaeddnlmeafrrdlygivygisdyglaqnlnisrkeaaefieryfesfpgvk
rymenivqeakqkgyvttllhrrrylpditsrnfnvrsfaermamntpiqgsaadiikka
midlnarlkeerlqahlllqvhdelileapkeemerlcrlvpevmeqavtlrvplkvdyh
ygstwydak

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3px4D (D:)
mespsseeekplakmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrf
flrpetaladpqfvawlgdetkkksmfdskraavalkwkgielcgvsfdlllaaylldpa
qgvddvaaaakmkqyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpflde
lrrneqdrllveleqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagq
efninspkqlgvilfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgklq
styiegllkvvrpatkkvhtifnqaltqtgrlsstepnlqnipirleegrkirqafvpse
sdwlifaadysqielrvlahiaeddnlmeafrrdldihtktamdifqvsedevtpnmrrq
akavnygivygisdyglaqnlnisrkeaaefieryfesfpgvkrymenivqeakqkgyvt
tllhrrrylpditsrnfnvrsfaermamntpiqgsaadiikkamidlnarlkeerlqahl
llqvhdelileapkeemerlcrlvpevmeqavtlrvplkvdyhygstwydak

    Sequence, based on observed residues (ATOM records): (download) 
    >3px4D (D:)
kmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrfflrpetaladpqf
vawlgdetkkksmfdskraavalkwkgielcgvsfdlllaaylldpaqgvddvaaaakmk
qyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpfldelrrneqdrllvel
eqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagqefninspkqlgvi
lfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgklqstyiegllkvvrp
atkkvhtifnqaltqtgrlsstepnlqnipirleegrkirqafvpsesdwlifaadysqi
elrvlahiaeddnlmeafrrdldihtktamdifqvsedevtpnmrrqakavnygivygis
dyglaqnlnisrkeaaefieryfesfpgvkrymenivqeakqkgyvttllhrrrylpdit
srnfnvrsfaermamntpiqgsaadiikkamidlnarlkeerlqahlllqvhdelileap
keemerlcrlvpevmeqavtlrvplkvdyhygstwydak

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.