7Z87: DNA-PK in the active state

DNA-PK in the active state. Determined by electron microscopy at 2.91 Å resolution. Released 18 Jan 2023.

Method
Electron microscopy
Resolution
2.91 Å
Organism
Homo sapiens
Chains
5
Atoms
39,708
Mol. weight
638.89 kDa
Ligands
1IX
Released
18 Jan 2023

Explore 7Z87 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z87 contains 266 α-helices and 68 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 220 helices, 19 β-strands

ElementResiduesLengthSheet
α-helix11-2010
α-helix27-4418
α-helix48-5811
α-helix65-717
α-helix76-783
α-helix79-9517
α-helix98-1036
α-helix104-11714
α-helix121-13717
α-helix143-1464
α-helix149-15911
α-helix171-18313
α-helix186-1883
α-helix193-20917
α-helix217-23014
α-helix244-25613
α-helix267-27812
α-helix284-2874
α-helix290-30112
α-helix308-32922
α-helix335-35016
α-helix356-37621
α-helix380-3834
α-helix387-39610
α-helix410-42112
α-helix432-44413
α-helix4501
α-helix454-46815
α-helix473-49119
α-helix525-5273
α-helix528-5347
α-helix560-57718
α-helix617-63317
α-helix643-6453
α-helix646-65813
α-helix666-67914
α-helix700-71718
α-helix718-7203
α-helix723-73513
α-helix745-7473
α-helix749-75810
α-helix763-77917
α-helix786-7927
α-helix793-7953
α-helix797-7993
α-helix817-8226
α-helix828-83811
α-helix848-86114
α-helix866-8694
α-helix877-8815
β-strand893-89531
β-strand904-90631
α-helix907-9093
α-helix911-9199
α-helix924-94522
α-helix959-97315
α-helix978-99518
α-helix1004-101714
α-helix1023-104220
α-helix1056-106712
α-helix1072-108514
α-helix1096-111520
α-helix1123-113816
α-helix1151-11544
α-helix1158-11592
α-helix1166-117510
α-helix1181-119414
α-helix1204-121512
α-helix1219-12224
α-helix1243-12453
α-helix1251-126616
α-helix1268-12725
α-helix1278-12825
α-helix1290-130011
α-helix1324-134926
α-helix1357-13593
α-helix1366-137611
α-helix1391-140616
α-helix1413-142210
α-helix1425-14317
α-helix1447-146115
α-helix1464-14674
α-helix1478-148912
α-helix1505-152117
α-helix1525-15328
α-helix1557-15626
α-helix1566-15738
α-helix1575-15839
α-helix1590-160617
α-helix1613-162412
α-helix1626-16283
α-helix1639-165517
α-helix1668-168013
α-helix1686-16938
α-helix1696-16983
α-helix1707-171812
α-helix1734-175219
α-helix1756-176611
α-helix1775-178612
α-helix1791-180616
α-helix1813-18186
α-helix1819-18246
α-helix1825-18306
α-helix1837-185115
α-helix1860-188223
α-helix1887-18904
α-helix1896-18994
α-helix1909-192315
α-helix1934-195219
α-helix19621
α-helix1963-19675
β-strand197012
α-helix1971-19733
β-strand197512
α-helix1978-19814
α-helix2035-204713
α-helix2094-210512
α-helix2125-21339
α-helix2140-215213
α-helix2154-21574
α-helix2158-21636
α-helix2166-21738
α-helix2185-219511
α-helix2206-222116
α-helix2228-224417
α-helix2256-22605
α-helix2271-228212
α-helix2285-22862
α-helix2296-230510
α-helix2306-23083
α-helix2313-233220
α-helix2338-235316
α-helix2357-237014
α-helix2372-23743
α-helix2375-238511
α-helix2386-23883
α-helix2392-240312
α-helix2412-24176
α-helix2420-24256
α-helix2429-244214
α-helix2443-24453
α-helix2448-245912
α-helix2467-248115
α-helix2495-250814
α-helix2509-25113
α-helix2517-252610
α-helix2535-25439
α-helix2548-25503
α-helix2551-256313
α-helix2736-276631
α-helix2788-279811
α-helix2802-281918
α-helix2826-284621
α-helix2852-286312
α-helix2866-28683
α-helix2873-288210
α-helix2886-289712
α-helix2920-293314
α-helix2945-29473
α-helix2951-296111
α-helix2965-297612
β-strand298213
β-strand298413
α-helix2988-300417
α-helix3008-30169
α-helix3034-30363
α-helix3041-305313
α-helix3061-30688
α-helix3073-30819
α-helix3085-30928
α-helix3096-311520
α-helix3125-31295
α-helix3132-314615
α-helix3155-316511
α-helix3169-31702
α-helix3176-319520
α-helix3227-324822
α-helix3252-32609
α-helix3270-328819
α-helix3296-330712
α-helix3320-334324
α-helix3347-33504
α-helix3356-33605
α-helix3372-339322
α-helix3410-342819
α-helix3434-34396
α-helix3442-345514
α-helix3459-34624
α-helix3467-34737
α-helix3481-34888
α-helix3492-34987
α-helix3499-35024
α-helix3515-352410
α-helix3530-35389
α-helix3548-356114
α-helix3567-357610
α-helix3581-359313
α-helix3605-361511
α-helix3621-36266
α-helix3633-36397
α-helix3642-36498
α-helix3651-36533
α-helix3661-367212
α-helix3681-36833
β-strand3719-372244
β-strand3727-372825
β-strand3736-373725
β-strand3739-374244
β-strand3747-374934
β-strand3750-375345
α-helix3759-377416
α-helix3779-37835
β-strand3793-379755
β-strand3800-380455
α-helix3805-38062
β-strand3809-381136
α-helix3812-38198
α-helix3822-38298
α-helix3835-384713
α-helix3854-38607
α-helix3864-387512
α-helix3882-38898
α-helix3894-391724
β-strand3928-393146
β-strand3937-393936
α-helix3956-39572
α-helix3965-39706
α-helix3979-399214
α-helix3996-40016
α-helix4004-40074
α-helix4039-404911
β-strand405417
α-helix4056-406813
α-helix4074-40829
α-helix4089-40924
β-strand409617
α-helix4100-411112
α-helix4114-41174
α-helix4122-41243
Chain B: 15 helices, 25 β-strands
ElementResiduesLengthSheet
β-strand35-4398
α-helix59-7719
β-strand82-8878
β-strand9019
β-strand9418
β-strand102-10988
α-helix113-1208
α-helix124-13411
β-strand13719
α-helix145-15511
β-strand161-170108
α-helix180-19516
β-strand198-20478
α-helix240-2434
β-strand258-262510
β-strand268-274710
β-strand277111
α-helix282-2854
β-strand286-289412
β-strand295112
β-strand298-303613
β-strand310113
α-helix311-3122
β-strand316-322714
β-strand325-329514
α-helix331-3366
β-strand344-352910
β-strand366-370510
α-helix378-39215
β-strand394-401810
β-strand409-416810
β-strand419115
β-strand428115
β-strand431-436610
α-helix437-4382
α-helix458-46912
β-strand470116
α-helix481-49515
α-helix511-5188
α-helix522-5265
Chain C: 31 helices, 24 β-strands
ElementResiduesLengthSheet
β-strand8-15817
α-helix22-243
α-helix30-4819
β-strand52-59817
β-strand77-79317
β-strand84117
α-helix88-958
α-helix108-12114
β-strand130-135617
α-helix141-1433
α-helix148-15710
β-strand160-165617
α-helix199-21618
α-helix218-2225
β-strand224-226317
α-helix227-2326
α-helix242-2432
β-strand246-253816
β-strand257-2681216
β-strand277-280414
β-strand290-295613
β-strand305113
α-helix307-3093
β-strand310-313412
β-strand314-316318
β-strand319-321318
α-helix326-3316
β-strand339-346816
α-helix353-3553
β-strand360-364516
α-helix372-38514
β-strand390-396716
α-helix402-4032
β-strand404-409616
β-strand419-423516
β-strand430111
α-helix445-4473
α-helix448-46013
β-strand462110
β-strand464-466319
β-strand473-475319
α-helix483-4842
α-helix485-49915
α-helix505-5095
α-helix510-5156
α-helix520-53617
α-helix550-5534
α-helix597-6048
α-helix613-62513
α-helix629-64820
α-helix652-66817
α-helix673-6819
α-helix696-6983
α-helix700-7045
α-helix725-7306

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA-dependent protein kinase catalytic subunitAprotein4128Homo sapiensP78527
X-ray repair cross-complementing protein 6Bprotein609Homo sapiensP12956 (AlphaFold model)
X-ray repair cross-complementing protein 5Cprotein732Homo sapiensP13010 (AlphaFold model)
DNA (26-mer)DDNA26Homo sapiens
DNA (26-mer)EDNA26Homo sapiens
Sequence of entity 1 (A), FASTA
>7Z87_1 DNA-dependent protein kinase catalytic subunit (chains 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
ARGSKDHNIRAQEPESGLSEETQVKCLMDQATDPNILGRTWEGWEPWM
Sequence of entity 2 (B), FASTA
>7Z87_2 X-ray repair cross-complementing protein 6 (chains B)
MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPF
DMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELD
QFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDS
AKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLE
DLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
RTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHH
YLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFEN
PVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKV
TKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELL
EALTKHFQD
Sequence of entity 3 (C), FASTA
>7Z87_3 X-ray repair cross-complementing protein 5 (chains C)
MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG
TDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQH
ETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGD
GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKI
ERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDD
DETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQ
VLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLV
YVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTT
KIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLI
EAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRV
LVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLK
ALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFE
EGGDVDDLLDMI
Sequence of entity 4 (D), FASTA
>7Z87_4 DNA (26-MER) (chains D)
CCCGCTGCCGATTCCGCTGGAACATT
Sequence of entity 5 (E), FASTA
>7Z87_5 DNA (26-MER) (chains E)
AATGTTCCAGCGGAATCGGCAGCGGG

Ligands and cofactors

IDNameFormulaCopies
1IX(~{S})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-m…C24 H21 Cl F N5 O31

Primary citation

Human DNA-dependent protein kinase activation mechanism. Liang, S., Blundell, T.L. Nat Struct Mol Biol (2023) 30:140-147. DOI 10.1038/s41594-022-00881-w · PubMed

Other PDB entries of the same protein (UniProt P78527), best resolution first:

Browse structure collections

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