PDB entry 6zha

View 6zha on RCSB PDB site
Description: cryo-em structure of dna-pk monomer
Deposited on 2020-06-21, released 2020-10-21
The last revision was dated 2021-01-20, with a file datestamp of 2021-01-15.
Experiment type: EM
Resolution: 3.91 Å
R-factor: N/A
AEROSPACI score: 0.09 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-PKcs
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P78527 (Start-4127)
    • PDB 6ZHA (4128-4155)
  • Chain 'B':
    Compound: X-ray repair cross-complementing protein 6
    Species: Homo sapiens [TaxId:9606]
    Gene: XRCC6, G22P1
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: X-ray repair cross-complementing protein 5
    Species: Homo sapiens [TaxId:9606]
    Gene: XRCC5, G22P2
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: DNA
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
  • Chain 'E':
    Compound: DNA
    Species: HOMO SAPIENS, synthetic [TaxId:9606]

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:
    >6zhaA (A:)
    magsgagvrcsllrlqetlsaadrcgaalaghqlirglgqecvlssspavlalqtslvfs
    rdfgllvfvrkslnsiefrecreeilkflciflekmgqkiapysveikntctsvytkdra
    akckipaldllikllqtfrssrlmdefkigelfskfygelalkkkipdtvlekvyellgl
    lgevhpseminnaenlfraflgelktqmtsavrepklpvlagclkglssllcnftksmee
    dpqtsreifnfvlkairpqidlkryavpsaglrlfalhasqfstclldnyvslfevllkw
    cahtnvelkkaalsalesflkqvsnmvaknaemhknklqyfmeqfygiirnvdsnnkels
    iairgyglfagpckvinakdvdfmyveliqrckqmfltqtdtgddrvyqmpsflqsvasv
    llyldtvpevytpvlehlvvmqidsfpqyspkmqlvccraivkvflalaakgpvlrncis
    tvvhqgliricskpvvlpkgpesesedhrasgevrtgkwkvptykdyvdlfrhllssdqm
    mdsiladeaffsvnssseslnhllydefvksvlkivekldltleiqtvgeqengdeapgv
    wmiptsdpaanlhpakpkdfsafinlvefcreilpekqaeffepwvysfsyelilqstrl
    plisgfykllsitvrnakkikyfegvspkslkhspedpekyscfalfvkfgkevavkmkq
    ykdellascltfllslphniieldvrayvpalqmafklglsytplaevglnaleewsiyi
    drhvmqpyykdilpcldgylktsalsdetknnwevsalsraaqkgfnkvvlkhlkktknl
    ssneaisleeirirvvqmlgslggqinknlltvtssdemmksyvawdrekrlsfavpfre
    mkpvifldvflprvtelaltasdrqtkvaacellhsmvmfmlgkatqmpeggqgappmyq
    lykrtfpvllrlacdvdqvtrqlyeplvmqlihwftnnkkfesqdtvalleaildgivdp
    vdstlrdfcgrcireflkwsikqitpqqqekspvntkslfkrlyslalhpnafkrlgasl
    afnniyrefreeeslveqfvfealviymeslalahadekslgtiqqccdaidhlcriiek
    khvslnkakkrrlprgfppsaslclldlvkwllahcgrpqtecrhksielfykfvpllpg
    nrspnlwlkdvlkeegvsflintfegggcgqpsgilaqptllylrgpfslqatlcwldll
    laalecyntfigertvgalqvlgteaqssllkavafflesiamhdiiaaekcfgtgaagn
    rtspqegerynyskctvvvrimeftttllntspegwkllkkdlcnthlmrvlvqtlcepa
    sigfnigdvqvmahlpdvcvnlmkalkmspykdilethlrekitaqsieelcavnlygpd
    aqvdrsrlaavvsackqlhragllhnilpsqstdlhhsvgtellslvykgiapgderqcl
    psldlsckqlasgllelafafgglcerlvslllnpavlstaslgssqgsvihfshgeyfy
    slfsetintellknldlavlelmqssvdntkmvsavlngmldqsfreranqkhqglklat
    tilqhwkkcdswwakdspletkmavlallakilqidssvsfntshgsfpevfttyislla
    dtkldlhlkgqavtllpfftsltggsleelrrvleqlivahfpmqsrefppgtprfnnyv
    dcmkkfldalelsqspmllelmtevlcreqqhvmeelfqssfrriarrgscvtqvglles
    vyemfrkddprlsftrqsfvdrslltllwhcsldalreffstivvdaidvlksrftklne
    stfdtqitkkmgyykildvmysrlpkddvhakeskinqvfhgscitegneltktliklcy
    daftenmagenqllerrrlyhcaayncaisviccvfnelkfyqgflfsekpeknllifen
    lidlkrrynfpvevevpmerkkkyieirkeareaangdsdgpsymsslsyladstlseem
    sqfdfstgvqsysyssqdprpatgrfrrreqrdptvhddvlelemdelnrhecmapltal
    vkhmhrslgppqgeedsvprdlpswmkflhgklgnpivplnirlflaklvinteevfrpy
    akhwlspllqlaasennggegihymvveivatilswtglatptgvpkdevlanrllnflm
    khvfhpkravfrhnleiiktlvecwkdclsipyrlifekfsgkdpnskdnsvgiqllgiv
    mandlppydpqcgiqsseyfqalvnnmsfvrykevyaaaaevlglilryvmerknilees
    lcelvakqlkqhqntmedkfivclnkvtksfppladrfmnavffllpkfhgvlktlclev
    vlcrvegmtelyfqlkskdfvqvmrhrdderqkvcldiiykmmpklkpvelrellnpvve
    fvshpsttcreqmynilmwihdnyrdpesetdndsqeifklakdvliqglidenpglqli
    irnfwshetrlpsntldrllalnslyspkievhflslatnfllemtsmspdypnpmfehp
    lsecefqeytidsdwrfrstvltpmfvetqasqgtlqtrtqegslsarwpvagqiratqq
    qhdftltqtadgrssfdwltgsstdplvdhtspssdsllfahkrserlqraplksvgpdf
    gkkrlglpgdevdnkvkgaagrtdllrlrrrfmrdqeklslmyarkgvaeqkrekeikse
    lkmkqdaqvvlyrsyrhgdlpdiqikhsslitplqavaqrdpiiakqlfsslfsgilkem
    dkfktlseknnitqkllqdfnrflnttfsffppfvsciqdiscqhaallsldpaavsagc
    laslqqpvgirlleeallrllpaelpakrvrgkarlppdvlrwvelaklyrsigeydvlr
    giftseigtkqitqsallaearsdyseaakqydealnkqdwvdgepteaekdfwelasld
    cynhlaewksleycstasidsenppdlnkiwsepfyqetylpymirsklklllqgeadqs
    lltfidkamhgelqkailelhysqelsllyllqddvdrakyyiqngiqsfmqnyssidvl
    lhqsrltklqsvqalteiqefisfiskqgnlssqvplkrllntwtnrypdakmdpmniwd
    diitnrcfflskieekltplpednsmnvdqdgdpsdrmevqeqeedisslirsckfsmkm
    kmidsarkqnnfslamkllkelhkesktrddwlvswvqsycrlshcrsrsqgcseqvltv
    lktvslldennvssylsknilafrdqnillgttyriianalssepaclaeieedkarril
    elsgsssedsekviaglyqrafqhlseavqaaeeeaqppswscgpaagvidaymtladfc
    dqqlrkeeenasvidsaelqaypalvvekmlkalklnsnearlkfprllqiierypeetl
    slmtkeissvpcwqfiswishmvalldkdqavavqhsveeitdnypqaivypfiissesy
    sfkdtstghknkefvarikskldqggviqdfinaldqlsnpellfkdwsndvraelaktp
    vnkkniekmyermyaalgdpkapglgafrrkfiqtfgkefdkhfgkggskllrmklsdfn
    ditnmlllkmnkdskppgnlkecspwmsdfkveflrneleipgqydgrgkplpeyhvria
    gfdervtvmaslrrpkriiirghderehpflvkggedlrqdqrveqlfqvmngilaqdsa
    csqralqlrtysvvpmtsrlgliewlentvtlkdlllntmsqeekaaylsdprappceyk
    dwltkmsgkhdvgaymlmykganrtetvtsfrkreskvpadllkrafvrmstspeaflal
    rshfasshalicishwilgigdrhlnnfmvametggvigidfghafgsatqflpvpelmp
    frltrqfinlmlpmketglmysimvhalrafrsdpglltntmdvfvkepsfdwknfeqkm
    lkkggswiqeinvaeknwyprqkicyakrklaganpavitcdelllghekapafrdyvav
    argskdhniraqepesglseetqvkclmdqatdpnilgrtwegwepwmxxxxxxxxxxxx
    xxxxxxxxxxxxxxxx
    

    Sequence, based on observed residues (ATOM records):
    >6zhaA (A:)
    csllrlqetlsaadrcgaalaghqlirglgqecvlssspavlalqtslvfsrdfgllvfv
    rkslnsiefrecreeilkflciflekmgqkiapysveikntctsvytkdraakckipald
    llikllqtfrssrlmdefkigelfskfygelalkkkipdtvlekvyellgllgevhpsem
    innaenlfraflgelktqmtsavrepklpvlagclkglssllcnftksmeedpqtsreif
    nfvlkairpqidlkryavpsaglrlfalhasqfstclldnyvslfevllkwcahtnvelk
    kaalsalesflkqvsnmvaknaemhknklqyfmeqfygiirnvdsnnkelsiairgyglf
    agpckvinakdvdfmyveliqrckqmfltqtdtgddrvyqmpsflqsvasvllyldtvpe
    vytpvlehlvvmqidsfpqyspkmqlvccraivkvflalaakgpvlrncistvvhqglir
    icskpvvlpwkvptykdyvdlfrhllssdqmmdsiladeaffsvnssseslnhllydefv
    ksvlkivekldltleiqmiptsdpaanlhpakpkdfsafinlvefcreilpekqaeffep
    wvysfsyelilqstrlplisgfykllsitvrnakkikyfegvspdpekyscfalfvkfgk
    evavkmkqykdellascltfllslphniieldvrayvpalqmafklglsytplaevglna
    leewsiyidrhvmqpyykdilpcldgylktsaaisleeirirvvqmlgslggqinknllt
    vtssdemmksyvawdrekrlsfavpfremkpvifldvflprvtelaltasdrqtkvaace
    llhsmvmfmlgkatqppmyqlykrtfpvllrlacdvdqvtrqlyeplvmqlihwftnnkk
    fesqdtvalleaildgivdpvdstlrdfcgrcireflkwsikqitpqqqekspvntkslf
    krlyslalhpnafkrlgaslafnniyrefreeeslveqfvfealviymeslalahadeks
    lgtiqqccdaidhlcriiekkhvslnkakkrrlprgfppsaslclldlvkwllahcgrpq
    tecrhksielfykfvpllpgnrspnlwlkdvlkeegvsflintfegggcgqpsgilaqpt
    llylrgpfslqatlcwldlllaalecyntfigertvgalqvlgteaqssllkavaffles
    iamhdiiaaekcfggnrtspqegerynyskctvvvrimeftttllntspegwkllkkdlc
    nthlmrvlvqtlcepasigfnigdvqvmahlpdvcvnlmkalkmspykdilethlrekit
    aqsieelcavnlygpdaqvdrsrlaavvsackqlhragllhnilpsqstdlhhsvgtell
    slvykgiapgderqclpsldlsckqlasgllelafafgglcerlvslllnpavlstsvih
    fshgeyfyslfsetintellknldlavlelmqssvdntkmvsavlngmldqsfreranqk
    hqglklattilqhwkkcdswwakdspletkmavlallakilqidssvsfntshgsfpevf
    ttyislladtkldlhlkgqavtllpfftsltggsleelrrvleqlivahfpmqsrefppg
    tprfnnyvdcmkkfldalelsqspmllelmtevlcreqqhvmeelfqssfrriarrgscv
    tqvgllesvyemfrkddprlsftrqsfvdrslltllwhcsldalreffstivvdaidvlk
    srftklnestfdtqitkkmgyykildvmysrlpkddvhakeskinqvfhgscitegnelt
    ktliklcydaftenmagenqllerrrlyhcaayncaisviccvfnelkfyqgflfsekpe
    knllifenlidlkrmdelnrhecmapltalvkhmhrslprdlpswmkflhgklgnpivpl
    nirlflaklvinteevfrpyakhwlspllqlaasennggegihymvveivatilswtgla
    tptgvpkdevlanrllnflmkhvfhpkravfrhnleiiktlvecwkdclsipyrlifekf
    sgkdpnskdnsvgiqllgivmandlppydpqcgiqsseyfqalvnnmsfvrykevyaaaa
    evlglilryvmerknileeslcelvakqlkqhqntmedkfivclnkvtksfppladrfmn
    avffllpkfhgvlktlclevvlcrvegmtelyfqlkskdfvqvmrhrdderqkvcldiiy
    kmmpklkpvelrellnpvvefvshpsttcreqmynilmwihdnyrdpesetdndsqeifk
    lakdvliqglidenpglqliirnfwshetrlpsntldrllalnslyspkievhflslatn
    fllemtsmspdypnpmfehplsecefqeytidsdwraqvvlyrsyrhgdlpdiqikhssl
    itplqavaqrdpiiakqlfsslfsgilkemdkfktlseknnitqkllqdfnrflnttfsf
    fppfvsciqdiscqhaallsldpaavsagclaslqqpvgirlleeallrllplppdvlrw
    velaklyrsigeydvlrgiftseigtkqitqsallaearsdyseaakqydealnkqdwvd
    gepteaekdfwelasldcynhlaewksleycstasidsenppdlnkiwsepfyqetylpy
    mirsklklllqgeadqslltfidkamhgelqkailelhysqelsllyllqddvdrakyyi
    qngiqsfmqnyssidvllhqsrltklqsvqalteiqefisfiskqgnlssqvplkrllnt
    wtnrypdakmdpmniwddiitnrcfflskieekldisslirsckfsmkmkmidsarkqnn
    fslamkllkelhkesktrddwlvswvqsycrlshcrsrsqgcseqvltvlktvslldenn
    vssylsknilafrdqnillgttyriianalssepaclaeieedkarrilelsgsssedse
    kviaglyqrafqhlseavqaaeeeaaagvidaymtladfcdqqlrkeeelqaypalvvek
    mlkalklnsnearlkfprllqiierypeetlslmtkeissvpcwqfiswishmvalldkd
    qavavqhsveeitdnypqaivypfiissesysfkdtstghknkefvarikskldqggviq
    dfinaldqlsnpellfkdwsndvraelaktpvnkkniekmyermyaalgdpkapglgafr
    rkfiqtfgkefdkhfgkggskllrmklsdfnditnmlllkmnkdskppgnlkecspwmsd
    fkveflrneleipgqydgrgkplpeyhvriagfdervtvmaslrrpkriiirghderehp
    flvkggedlrqdqrveqlfqvmngilaqdsacsqralqlrtysvvpmtsrlgliewlent
    vtlkdlllntmsqeekaaylsdprappceykdwltkmsgkhdvgaymlmykganrtetvt
    sfrkreskvpadllkrafvrmstspeaflalrshfasshalicishwilgigdrhlnnfm
    vametggvigidfghafgsatqflpvpelmpfrltrqfinlmlpmketglmysimvhalr
    afrsdpglltntmdvfvkepsfdwknfeqkmlkkggswiqeinvaeknwyprqkicyakr
    klaganpavitcdelllghekapafrdyvavargskdhniraqepesglseetqvkclmd
    qatdpnilgrtwegwepwmxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6zhaB (B:)
    msgwesyyktegdeeaeeeqeenleasgdykysgrdsliflvdaskamfesqsedeltpf
    dmsiqciqsvyiskiissdrdllavvfygtekdknsvnfkniyvlqeldnpgakrileld
    qfkgqqgqkrfqdmmghgsdyslsevlwvcanlfsdvqfkmshkrimlftnednphgnds
    akasrartkagdlrdtgifldlmhlkkpggfdislfyrdiisiaededlrvhfeesskle
    dllrkvraketrkralsrlklklnkdivisvgiynlvqkalkpppiklyretnepvktkt
    rtfntstgglllpsdtkrsqiygsrqiilekeeteelkrfddpglmlmgfkplvllkkhh
    ylrpslfvypeeslvigsstlfsallikclekevaalcrytprrnippyfvalvpqeeel
    ddqkiqvtppgfqlvflpfaddkrkmpftekimatpeqvgkmkaiveklrftyrsdsfen
    pvlqqhfrnlealaldlmepeqavdltlpkveamnkrlgslvdefkelvyppdynpegkv
    tkrkhdnegsgskrpkveyseeelkthiskgtlgkftvpmlkeacrayglksglkkqell
    ealtkhfqd
    

    Sequence, based on observed residues (ATOM records):
    >6zhaB (B:)
    ysgrdsliflvdaskamfesqsedeltpfdmsiqciqsvyiskiissdrdllavvfygte
    kdknsvnfkniyvlqeldnpgakrileldqfkgqqgqkrfqdmmghgsdyslsevlwvca
    nlfsdvqfkmshkrimlftnednphgndsakasrartkagdlrdtgifldlmhlkkpggf
    dislfyrdiisskledllrkvraketrkralsrlklklnkdivisvgiynlvqkalkppp
    iklyretnepvktktrtfntstgglllpsdtkrsqiygsrqiilekeeteelkrfddpgl
    mlmgfkplvllkkhhylrpslfvypeeslvigsstlfsallikclekevaalcrytprrn
    ippyfvalvpqeeelddqkiqvtppgfqlvflpfaddkrkmpftekimatpeqvgkmkai
    veklrftyrsdsfenpvlqqhfrnlealaldlmepeqavdltlpkveamnkrlgslvdef
    kelvyppdy
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6zhaC (C:)
    mvrsgnkaavvlcmdvgftmsnsipgiespfeqakkvitmfvqrqvfaenkdeialvlfg
    tdgtdnplsggdqyqnitvhrhlmlpdfdlledieskiqpgsqqadfldalivsmdviqh
    etigkkfekrhieiftdlssrfsksqldiiihslkkcdislqfflpfslgkedgsgdrgd
    gpfrlgghgpsfplkgiteqqkegleivkmvmislegedgldeiysfseslrklcvfkki
    erhsihwpcrltigsnlsiriaayksilqervkktwtvvdaktlkkediqketvyclndd
    detevlkediiqgfrygsdivpfskvdeeqmkyksegkcfsvlgfckssqvqrrffmgnq
    vlkvfaarddeaaavalsslihalddldmvaivryaydkranpqvgvafphikhnyeclv
    yvqlpfmedlrqymfsslknskkyapteaqlnavdalidsmslakkdektdtledlfptt
    kipnprfqrlfqcllhralhpreplppiqqhiwnmlnppaevttksqiplskiktlfpli
    eakkkdqvtaqeifqdnhedgptakklkteqggahfsvsslaegsvtsvgsvnpaenfrv
    lvkqkkasfeeasnqlinhieqfldtnetpyfmksidcirafreeaikfseeqrfnnflk
    alqekveikqlnhfweivvqdgitlitkeeasgssvtaeeakkflapkdkpsgdtaavfe
    eggdvddlldmi
    

    Sequence, based on observed residues (ATOM records):
    >6zhaC (C:)
    nkaavvlcmdvgftmsnsipgiespfeqakkvitmfvqrqvfaenkdeialvlfgtdgtd
    nplsggdqyqnitvhrhlmlpdfdlledieskiqpgsqqadfldalivsmdviqhetigk
    kfekrhieiftdlssrfsksqldiiihslkkcdislqfflpfslggpfrlgghgpsfplk
    giteqqkegleivkmvmislegedgldeiysfseslrklcvfkkierhsihwpcrltigs
    nlsiriaayksilqervkktwtvvdaktlkkediqketvyclndddetevlkediiqgfr
    ygsdivpfskvdeeqmkyksegkcfsvlgfckssqvqrrffmgnqvlkvfaarddeaaav
    alsslihalddldmvaivryaydkranpqvgvafphikhnyeclvyvqlpfmedlrqymf
    sslknskkyapteaqlnavdalidsmslakkdektdtledlfpttkipnprfqrlfqcll
    hralhpreplppiqqhiwnmlnppaevttksqiplskiktlfplieakkkdqvtaqeif
    

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    No sequence available.