PDB entry 4ds5

View 4ds5 on RCSB PDB site
Description: Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mg2+
Class: Transferase/DNA
Keywords: DNA Polymerase I, Transferase-DNA complex
Deposited on 2012-02-17, released 2012-06-06
The last revision prior to the SCOPe 2.08 freeze date was dated 2012-11-21, with a file datestamp of 2012-11-16.
Experiment type: XRAY
Resolution: 1.68 Å
R-factor: 0.177
AEROSPACI score: 0.57 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA polymerase
    Species: Geobacillus kaustophilus [TaxId:235909]
    Gene: polA, GK2730
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5KWC1 (Start-591)
      • engineered mutation (313)
      • see remark 999 (538)
    Domains in SCOPe 2.08: d4ds5a1, d4ds5a2
  • Chain 'B':
    Compound: DNA (5'-d(*cp*cp*tp*gp*ap*cp*tp*cp*c)-3')
  • Chain 'C':
    Compound: DNA (5'-d(*cp*ap*tp*gp*gp*gp*ap*gp*tp*cp*ap*gp*g)-3')
  • Chain 'D':
    Compound: DNA polymerase
    Species: Geobacillus kaustophilus [TaxId:235909]
    Gene: polA, GK2730
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5KWC1 (Start-591)
      • engineered mutation (313)
      • see remark 999 (538)
    Domains in SCOPe 2.08: d4ds5d1, d4ds5d2
  • Chain 'E':
    Compound: DNA (5'-d(*cp*cp*tp*gp*ap*cp*tp*cp*c)-3')
  • Chain 'F':
    Compound: DNA (5'-d(*cp*ap*tp*gp*gp*gp*ap*gp*tp*cp*ap*gp*g)-3')
  • Heterogens: SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4ds5A (A:)
mespsseeekplakmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrf
flrpetaladpqfvawlgdetkkksmfdskraavalkwkgielcgvsfdlllaaylldpa
qgvddvaaaakmkqyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpflde
lrrneqdrllveleqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagq
efninspkqlgvilfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgklq
styiegllkvvrpatkkvhtifnqaltqtgrlsstepnlqnipirleegrkirqafvpse
sdwlifaadysqielrvlahiaeddnlmeafrrdldihtktamdifqvsedevtpnmrrq
akavnfgivygisdyglaqnlnisrkeaaefieryfesfpgvkrymenivqeakqkgyvt
tllhrrrylpditsrnfnvrsfaermamntpiqgsaadiikkamidlnarlkeerlqahl
llqvhdelileapkeemerlcrlvpevmeqavtlrvplkvdyhygstwydak

    Sequence, based on observed residues (ATOM records): (download) 
    >4ds5A (A:)
akmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrfflrpetaladpq
fvawlgdetkkksmfdskraavalkwkgielcgvsfdlllaaylldpaqgvddvaaaakm
kqyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpfldelrrneqdrllve
leqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagqefninspkqlgv
ilfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgklqstyiegllkvvr
patkkvhtifnqaltqtgrlsstepnlqnipirleegrkirqafvpsesdwlifaadysq
ielrvlahiaeddnlmeafrrdldihtktamdifqvsedevtpnmrrqakavnfgivygi
sdyglaqnlnisrkeaaefieryfesfpgvkrymenivqeakqkgyvttllhrrrylpdi
tsrnfnvrsfaermamntpiqgsaadiikkamidlnarlkeerlqahlllqvhdelilea
pkeemerlcrlvpevmeqavtlrvplkvdyhygstwydak

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4ds5D (D:)
mespsseeekplakmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrf
flrpetaladpqfvawlgdetkkksmfdskraavalkwkgielcgvsfdlllaaylldpa
qgvddvaaaakmkqyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpflde
lrrneqdrllveleqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagq
efninspkqlgvilfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgklq
styiegllkvvrpatkkvhtifnqaltqtgrlsstepnlqnipirleegrkirqafvpse
sdwlifaadysqielrvlahiaeddnlmeafrrdldihtktamdifqvsedevtpnmrrq
akavnfgivygisdyglaqnlnisrkeaaefieryfesfpgvkrymenivqeakqkgyvt
tllhrrrylpditsrnfnvrsfaermamntpiqgsaadiikkamidlnarlkeerlqahl
llqvhdelileapkeemerlcrlvpevmeqavtlrvplkvdyhygstwydak

    Sequence, based on observed residues (ATOM records): (download) 
    >4ds5D (D:)
lakmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrfflrpetaladp
qfvawlgdetkkksmfdskraavalkwkgielcgvsfdlllaaylldpaqgvddvaaaak
mkqyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpfldelrrneqdrllv
eleqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagqefninspkqlg
vilfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgklqstyiegllkvv
rpatkkvhtifnqaltqtgrlsstepnlqnipirleegrkirqafvpsesdwlifaadys
qielrvlahiaeddnlmeafrrdldihtktkavnfgivygisdyglaqnlnisrkeaaef
ieryfesfpgvkrymenivqeakqkgyvttllhrrrylpditsrnfnvrsfaermamntp
iqgsaadiikkamidlnarlkeerlqahlllqvhdelileapkeemerlcrlvpevmeqa
vtlrvplkvdyhygstwydak

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.