PDB entry 6hms

View 6hms on RCSB PDB site
Description: cryo-em map of dna polymerase d from pyrococcus abyssi in complex with dna
Deposited on 2018-09-12, released 2019-01-30
The last revision was dated 2019-12-11, with a file datestamp of 2019-12-06.
Experiment type: EM
Resolution: N/A
R-factor: N/A
AEROSPACI score: -0.3 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA polymerase II small subunit
    Species: Pyrococcus abyssi [TaxId:29292]
    Gene: polB, PYRAB01210, PAB2266
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9V2F3 (5-399)
      • expression tag (0-4)
      • conflict (231)
  • Chain 'B':
    Compound: DNA polymerase II large subunit,DNA polymerase II large subunit
    Species: Pyrococcus abyssi [TaxId:29292]
    Gene: polC, PYRAB01200, PAB2404
    Database cross-references and differences (RAF-indexed):
  • Chain 'P':
    Compound: DNA (5'-d(*gp*ap*gp*ap*cp*gp*gp*gp*cp*cp*gp*cp*gp*tp*c)-3')
    Species: Pyrococcus abyssi, synthetic [TaxId:29292]
  • Chain 'T':
    Compound: DNA (5'-d(p*tp*gp*ap*cp*gp*cp*gp*gp*cp*cp*cp*gp*tp*cp*tp*c)-3')
    Species: Pyrococcus abyssi, synthetic [TaxId:29292]
  • 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; same for both SEQRES and ATOM records:
    >6hmsA (A:)
    yevkfveayaslfksrlsklkrilrenpeisnvvdigklnyvsgdeevtiiglvnskret
    nrglifevedktgivkvflpkdsedyreafkvlpdavvafkgfyskkgiffankfylpdv
    plyrkqkppleekvyailisdihvgsrefcekaflkflewlnghveskeeeeivsrvkyl
    iiagdvvdgigiypgqysdlvipdifdqyealanllanvpehitmfigpgnadaarpaip
    qpefykeyakpiyklknaiiisnpavirlhgrdfliahgrgiedvvsfvpglthhkpglp
    mvellkmrhlaptfggkvpiapdpedllvieevpdlvqmghvhvydavvyrgvqlvnsat
    wqaqtefqkmvnivptpakvpvvdvesarvvkvldfsgwc
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6hmsB (B:)
    melpkemeeyfemlqreidkayeiakkaraqgkdpsldveipqatdmagrveslvgppgv
    akrirelvkeygkeiaalkivdeiiegkfgdlgsrekyaeqavrtalailtegivsapie
    gianvkikrntwadnseylalyyagpirssggtaqalsvlvgdyvrrklgldrfkpsekh
    iermveevdlyhravtrlqyhpspeevrlamrnipieitgeatddvevshrdvpgvetnq
    lrggailvlaegvlqkakklvkyidkmgiegwewlkefveakekgepkeegkeeslaest
    leetkvevdmgfyyslyqkfkeeiapsdkyakeviggrplfsdpskpggfrlrygrsras
    gfatwginpatmilvdeflaigtqlkterpgkgavvtpvttiegpivklkdgsvlrvddy
    nlalkvredveeilylgdaviafgdfvennqtllpanyceewwilefvkalkeiyevhle
    pfteneeesieeasdyleidpeflkemlrdplrvkppvelaihfsevlgiplhpyytlyw
    nsvepkdveklwrllknyaeiewsnfrgikfakkivisqeklgdskrtlellglphtvrd
    gnvivdypwaaalltplgnlnwefmakplyatidiinenneiklrdrgiswigarmgrpe
    kakerkmkppvqvlfpiglaggssrdikkaaeegkvaeveiaffkcpkcghvgpehlcpn
    cgtrkellwvcprcnaeypesqaegynytcpkcnvklrpyakrkirpsellnramenvkv
    ygvdklkgvmgmtsgwkmpeplekgllrakndvyvfkdgtirfdatdapithfrpreigv
    sveklrelgythdfegkplvsedqivelkpqdiilskeagryllkvakfvddllekfygl
    prfynaekmedlighlviglaphtsagivgriigfvdalvgyahpyfhaakrrncdgded
    avmllldallnfsryylpekrggkmdaplvittrldprevdsevhnmdivryyplefyea
    tyelkspkelvgviervedrlgkpemyyglkfthdtddialgpkmslykqlgdmeekvrr
    qlevakriravdehgvaekilnshlipdlrgnlrsftrqefrcvkcntkfrrpplngkcp
    vcggkivltvskgaiekylgtakmlvteynvknytrqriclterdidslfenvfpetqlt
    livnpndicqrlvmartgevnksgllenlsngskktekaekaekprkksdekpkkkrvis
    leeffsrksk
    

    Sequence, based on observed residues (ATOM records):
    >6hmsB (B:)
    pkemeeyfemlqreidkayeiakkaraqgkdpsldveipqatdmagrveslvgppgvakr
    irelvkeygkeiaalkivdeiiegkfgdlgsrekyaeqavrtalailtegivsapiegia
    nvkikrntwadnseylalyyagpirssggtaqalsvlvgdyvrrklgldrfkpsekhier
    mveevdlyhravtrlqyhpspeevrlamrnipieitgeatddvevshrdvpgvetnqlrg
    gailvlaegvlqkakklvkyidkmgiegwewlkefveakedmgfyyslyqkfkeeiapsd
    kyakeviggrskpggfrlrygrsrasgfatwginpatmilvdeflaigtqlkterpgkga
    vvtpvttiegpivklkdgsvlrvddynlalkvredveeilylgdaviafgdfvennqtll
    panyceewwilefvkalkeiyevhlepfteneeesieeasdyleidpeflkemlrdplrv
    kppvelaihfsevlgiplhpyytlywnsvepkdveklwrllknyaeiewsnfrgikfakk
    ivisqeklgdskrtlellglphtvrdgnvivdypwaaalltplgnlnwefmakplyatid
    iinenneiklrdrgiswigarmgrpekakerkmkppvqvlfpiglaggssrdikkaaeeg
    kvaeveiaffkcpkcghvgpehlcpncgtrkellwvcprcnaeypesqaegynytcpkcn
    vklrpyakrkirpsellnramenvkvygvdklkgvmgmtsgwkmpeplekgllrakndvy
    vfkdgtirfdatdapithfrpreigvsveklrelgythdfegkplvsedqivelkpqdii
    lskeagryllkvakfvddllekfyglprfynaekmedlighlviglaphtsagivgriig
    fvdalvgyahpyfhaakrrncdgdedavmllldallnfsryylpekrggkmdaplvittr
    ldpryyplefyeatyelkspkelvgviervedmeekvrrqlevakriravdehgvaekil
    nshlipdlrgnlrsftrqefrcvkcntkfrrpplngkcpvcggkivltekylgtakmlvt
    eynqriclterdidslfenvf
    

  • Chain 'P':
    No sequence available.

  • Chain 'T':
    No sequence available.