PDB entry 6knb

View 6knb on RCSB PDB site
Description: pold-pcna-dna (form a)
Deposited on 2019-08-05, released 2020-08-05
The last revision was dated 2021-02-17, with a file datestamp of 2021-02-12.
Experiment type: EM
Resolution: 6.9 Å
R-factor: N/A
AEROSPACI score: -0.02 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA polymerase II small subunit
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Gene: polB, TK1902
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: DNA polymerase D DP2 (DNA polymerase II large) subunit
    Species: Thermococcus kodakarensis [TaxId:311400]
    Database cross-references and differences (RAF-indexed):
    • PDB 6KNB
  • Chain 'C':
    Compound: DNA polymerase sliding clamp 1
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Gene: pcn1, TK0535
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: DNA polymerase sliding clamp 1
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Gene: pcn1, TK0535
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: DNA polymerase sliding clamp 1
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Gene: pcn1, TK0535
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: pri25DNA
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'G':
    Compound: temp35DNA
    Species: synthetic construct, synthetic [TaxId:32630]
  • Heterogens: FE, ZN

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6knbA (A:)
    mlvedllknnylitpsayyllsdhykkaftlaelikfaknrgtfvvdsnlareflaekgi
    issgivygdygvpiayvadetpeeekaystysdlviapkegfhyrakeipdewelafdvk
    nvkfevpkvknaqskegeviiqayssyfksrlkkmrrifrenpeigtivdiaklsyvred
    dvtiiglvnekretrkgylfeiedatgrikvfigsdkeganeaystimpdsvvafrgtpg
    kgiffanrvflpdvpkfkrskppleekvyaillsdihvgsnkfceeafikflewlngevn
    srteeelvsrikyiiiggdvvdgvgiypgqynelaipdifdqyealanllkqvpdhitmf
    igpgnhdaartalpqpgfyeeyakplyklknaviisnpavirlhgrdflvahgrgiedvv
    dfvpnrshhrpaeamvellklrhiaptfgnkvpiapdpedtlviesvpdlfqaghvhvmq
    yktyngvfvintgtwqaqtefqkmvniiptparvpiidvetarlravvrfdqfcegv
    

    Sequence, based on observed residues (ATOM records):
    >6knbA (A:)
    ystysdlviapkegfhyrakeipdewelafdvknvkfevpkvknaqskegeviiqayssy
    fksrlkkmrrifrenpeigtivdiaklsyvreddvtiiglvnekretrkgylfeiedatg
    rikvfigsdkeganeaystimpdsvvafrgtpgkgiffanrvflpdvpkfkrskppleek
    vyaillsdihvgsnkfceeafikflewlngevnsrteeelvsrikyiiiggdvvdgvgiy
    pgqynelaipdifdqyealanllkqvpdhitmfigpgnhdaartalpqpgfyeeyakply
    klknaviisnpavirlhgrdflvahgrgiedvvdfvpnrshhrpaeamvellklrhiapt
    fgnkvpiapdpedtlviesvpdlfqaghvhvmqyktyngvfvintgtwqaqtefqkmvni
    iptparvpiidvetarlravvrfdqfcegv
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6knbB (B:)
    mseeiyspemkayfeslqreidrayaiarkaraqgkdpsfdvevpqatdmagrveslvgp
    pgvaerirelvkeygkeiaalkvvdeiiegkfgdlgskekyaeqavrtalailtegivsa
    plegiadvkikrnewadgseylalyyagpirssggtaqalsvlvgdyvrrklgldrfkps
    dehiermveevdlyhravtrlqyhpeadevrlamrnipieitgeetdkvevshrnvpgve
    tnhlrggailvlaegvlqkakklvkyidkmgiegwdwikefveakekgksseenkdeska
    edtgtesvaekkenvekgfyyelyekfraniapnkkytkeiiggrplfaepstnggfrlr
    ygrsrvsgfatwsvnpatmlildefiaigtqmkterpgkgcivtpattvegpivrlkngs
    vvrvddyetalkvrnevdeilyvgdalvnfgdfvennqtllpanyveewwvqelvqaikd
    lyevelqpfaendreaveeaaeylevdpdflwnllkdplrvkpdvetaihlstvldipfh
    pyytlywntlqpeeveelqkallgaqiewaefrknrfakkvvlendknikrylellglph
    rlervekkrkvivveypwsaalltplgnlewefkakpfytvidiinennriklrdrgisw
    igarmgrpekakerkmkppvqvlfpiglaggqsrdikkaaeegktarveiaffkcpkcgh
    vgpehlcpvcgtrkellwhcpkcgadypesdakdfnyrcpkcdvelkpyaereikpadll
    rqamdnvkvygidrlkgvkgmtsgykmaeplekgllrvkndvyvfkdgtirfdatdapit
    hfkpkeigtsveklrelgythdfegkplerddqilelkvqdvilpyeagryllkvarfid
    dllekfyglprfynaekmedlvghlviglaphtsagiigriigfsdvlvgyahpyyhaak
    rrncdgdedavmllldallnfskyylpekrggkmdaplvvttrldprevdsevhnmdvvr
    yyplefykatyelkspkevkviervedrlgkpemyegikfthdtddiglgpkmslykqlg
    dmeekvarqlalaeriravdehhvaetiinshlvpdlrgnlrsftrqefrcvkcntkyrr
    ppltgkcpkcggkivltvskgaiekylptakmlvtkyrvkdytrqricitekdiktlfen
    vfpekqrtlmgfsadicekmvkertghsngkngyldefngkngkaskksgslasklsgkg
    kepskkkesakpkrsekvknltsfeaaakneqargtagnakkaesekpkrkkrkgislde
    ffgs
    

    Sequence, based on observed residues (ATOM records):
    >6knbB (B:)
    pemkayfeslqreidrayaiarkaraqgkdpsfdvevpqatdmagrveslvgppgvaeri
    relvkeygkeiaalkvvdeiiegkfgdlgskekyaeqavrtalailtegivsaplegiad
    vkikrnewadgseylalyyagpirssggtaqalsvlvgdyvrrklgldrfkpsdehierm
    veevdlyhravtrlqyhpeadevrlamrnipieitgeetdkvevshrnvpgvetnhlrgg
    ailvlaegvlqkakklvkyidkmgiegwdwikefveakekgvekgfyyelyekfraniap
    nkkytkeiiggrplfaepstnggfrlrygrswsvnpatmlilgcivtpattvegpivrlk
    ngsvvrvddyetalkvrnevdeilyvgdalvnfgdfvennqtllpanyveewwvqelvqa
    ikdlyevelqpfaendreaveeaaeylevdpdflwnllkdplrvkpdvetaihlstvldi
    pfhpyytlywntlqpeeveelqkallgaqiewaefrknrfakkvvlendknikrylellg
    lphrlervekkrkvivveypwsaalltplgnlewefkakpfytvidiinennriklrdrg
    iswigkppvqvlfpiglaggqsrdikkaaeegktarveiaffkcpkcghvgpehlcpvcg
    trkellwhcpkcgadypesdakdfnyrcpkcdvelkpyaereikpadllrqamdnvkvyg
    idrlkgvkgmtsgykmaeplekgllrvkndvyvfkdgtirfdatdapithfkpkeigtsv
    eklrelgythdfegkplerddqilelkvqdvilpyeagryllkvarfiddllekfyglpr
    fynaekmedlvghlviglaphtsagiigriigfsdvlvgyahpyyhaakrrncdgdedav
    mllldallnfskyylpekrggkmdaplvvttrldprevdsevhnmdvvryyplefykaty
    elkspkevkviervedgdmeekvarqlalaeriravdehhvaetiinshlvpdlrgnlrs
    ftrqefrcvkcntkyrrppltgkcpkcggkivltvskgaiekylptakmlvtkyrvkdyt
    rqricitekdiktlfekqrtlmgfsadicekmvkertghs
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records:
    >6knbC (C:)
    mpfevvfdgakefadliatasnlideaafkfteegismramdpsrvvlidlnlpesifsk
    yeveepetiginmdqfkkilkrgkakdtlilrkgdenfleitfegtakrtfrlplidvee
    lelelpelpftakvvllgevlkegikdaslvsdaikfiakeneftmkaegetneveirlt
    ledeglldleveeetksaygirylsdmvkgigkadevilrfgnemplqmeymirdegrlt
    fllaprvee
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records:
    >6knbD (D:)
    mpfevvfdgakefadliatasnlideaafkfteegismramdpsrvvlidlnlpesifsk
    yeveepetiginmdqfkkilkrgkakdtlilrkgdenfleitfegtakrtfrlplidvee
    lelelpelpftakvvllgevlkegikdaslvsdaikfiakeneftmkaegetneveirlt
    ledeglldleveeetksaygirylsdmvkgigkadevilrfgnemplqmeymirdegrlt
    fllaprvee
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records:
    >6knbE (E:)
    mpfevvfdgakefadliatasnlideaafkfteegismramdpsrvvlidlnlpesifsk
    yeveepetiginmdqfkkilkrgkakdtlilrkgdenfleitfegtakrtfrlplidvee
    lelelpelpftakvvllgevlkegikdaslvsdaikfiakeneftmkaegetneveirlt
    ledeglldleveeetksaygirylsdmvkgigkadevilrfgnemplqmeymirdegrlt
    fllaprvee
    

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    No sequence available.