7Z88: DNA-PK in the intermediate state

DNA-PK in the intermediate state. Determined by electron microscopy at 3.33 Å resolution. Released 18 Jan 2023.

Method
Electron microscopy
Resolution
3.33 Å
Organism
Homo sapiens
Chains
5
Atoms
38,754
Mol. weight
638.89 kDa
Ligands
1IX
Released
18 Jan 2023

Explore 7Z88 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z88 contains 248 α-helices and 70 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: 206 helices, 16 β-strands

ElementResiduesLengthSheet
α-helix10-178
α-helix26-4419
α-helix48-5811
α-helix65-717
α-helix80-9516
α-helix101-11616
α-helix121-1244
α-helix126-13712
α-helix149-15810
α-helix170-18314
α-helix193-20816
α-helix217-23115
α-helix244-25613
α-helix267-27812
α-helix279-2813
α-helix284-2874
α-helix290-30112
α-helix308-32720
α-helix335-35016
α-helix359-37315
α-helix380-3834
α-helix387-3937
α-helix394-3985
α-helix410-42213
α-helix432-44413
α-helix454-46815
α-helix473-49018
α-helix528-5358
α-helix560-57718
β-strand58311
β-strand61411
α-helix617-63317
α-helix646-65914
α-helix666-67914
α-helix701-71717
α-helix718-7203
α-helix723-73311
α-helix745-7473
α-helix750-7578
α-helix763-77816
α-helix817-8237
α-helix829-8368
α-helix845-8473
α-helix848-86114
α-helix867-8704
β-strand893-89532
β-strand904-90632
α-helix908-9103
α-helix911-9199
α-helix924-94421
α-helix959-97315
α-helix979-9824
α-helix985-99511
α-helix998-10003
α-helix1004-101714
α-helix1023-104321
α-helix1056-106712
α-helix1075-108511
α-helix1102-11043
α-helix1105-11139
α-helix1119-11213
α-helix1123-114422
α-helix1151-11533
α-helix1166-11749
α-helix1181-119414
α-helix1204-121411
α-helix1218-12258
α-helix1251-127121
α-helix1278-12814
α-helix1284-12863
α-helix1290-129910
α-helix1326-134924
α-helix1356-13583
α-helix1368-13769
α-helix1379-13824
α-helix1390-140819
α-helix1413-142210
α-helix1425-14317
α-helix1441-146020
α-helix1478-149013
α-helix1506-152116
α-helix1525-15339
α-helix1557-15637
α-helix1566-15716
α-helix1578-15847
α-helix1590-160617
α-helix1614-162411
α-helix1641-165515
α-helix1668-167811
α-helix1686-16927
α-helix1696-16994
α-helix1704-172118
α-helix1736-175217
α-helix1756-176611
α-helix1775-178612
α-helix1791-180616
α-helix1813-18197
α-helix1820-18245
α-helix1825-18306
α-helix1838-185114
α-helix1860-188324
α-helix1887-18904
α-helix1910-192011
α-helix1934-195219
α-helix1961-19644
α-helix1971-19733
α-helix1977-19815
α-helix2038-20458
α-helix2094-210512
α-helix2126-21349
α-helix2140-215213
α-helix2154-21574
α-helix2166-21738
α-helix2183-219513
α-helix2206-222116
α-helix2228-224417
α-helix2256-22605
α-helix2271-228212
α-helix2296-230712
β-strand231013
β-strand231213
α-helix2313-233220
α-helix2338-235316
α-helix2357-236812
α-helix2379-23857
α-helix2386-23883
α-helix2392-240211
α-helix2412-24176
α-helix2420-24234
α-helix2429-244113
α-helix2443-24453
α-helix2448-245912
α-helix2467-248216
α-helix2494-250714
α-helix2517-252610
α-helix2537-25426
α-helix2543-25453
α-helix2554-256411
α-helix2792-27976
α-helix2802-281918
α-helix2826-284621
α-helix2852-286110
α-helix2867-28693
α-helix2873-288311
α-helix2886-289611
α-helix2918-293013
α-helix2936-29405
α-helix2952-296110
α-helix2967-297610
α-helix2985-29873
α-helix2988-300417
α-helix3008-301710
α-helix3035-305521
α-helix3061-30677
α-helix3073-30819
α-helix3085-30928
α-helix3096-311419
α-helix3124-314421
α-helix3148-31514
α-helix3155-316612
α-helix3169-31702
α-helix3176-319520
α-helix3228-324821
α-helix3252-326312
α-helix3270-328718
α-helix3293-33019
α-helix3305-33084
α-helix3320-334122
α-helix3355-33617
α-helix3373-339018
α-helix3408-342720
α-helix3442-345413
α-helix3460-34623
α-helix3465-347410
α-helix3481-34888
α-helix3496-34983
α-helix3499-35057
α-helix3511-35144
α-helix3516-35249
α-helix3536-35394
α-helix3548-356215
α-helix3568-357811
α-helix3581-359515
α-helix3605-361410
α-helix3621-36266
α-helix3631-36366
α-helix3642-36465
α-helix3647-36515
α-helix3661-367313
α-helix3681-36833
α-helix3685-36884
α-helix3717-37193
β-strand372714
β-strand3736-373834
β-strand374115
β-strand374715
β-strand3750-375454
α-helix3759-377719
α-helix3779-37835
β-strand3793-379754
β-strand3800-380454
α-helix3805-38062
β-strand3809-381136
α-helix3812-38198
α-helix3822-38298
α-helix3835-384713
α-helix3854-38585
α-helix3864-387714
α-helix3883-38897
α-helix3894-391724
α-helix3925-39273
β-strand3928-393146
β-strand3937-393936
α-helix3965-39717
α-helix3982-399110
α-helix3997-400610
α-helix4040-404910
α-helix4056-406712
α-helix4074-40829
α-helix4100-411112
α-helix4114-41174
α-helix4122-41243
Chain B: 15 helices, 24 β-strands
ElementResiduesLengthSheet
β-strand37-4377
α-helix59-7719
β-strand82-8877
β-strand102-10437
β-strand10917
α-helix113-1208
α-helix124-13411
α-helix145-15511
β-strand164-16967
β-strand17018
α-helix181-19515
β-strand198-20147
β-strand20418
β-strand258-26259
β-strand268-27479
β-strand277110
α-helix282-2843
β-strand287-289311
β-strand295111
β-strand297-303712
α-helix313-3153
β-strand318-322513
β-strand325-329513
α-helix331-3377
β-strand345-35289
β-strand367-37049
α-helix378-39114
β-strand394-40079
β-strand409-41359
β-strand416114
β-strand431114
β-strand434-43639
α-helix437-4382
α-helix458-46912
β-strand470115
α-helix481-49414
α-helix500-5012
α-helix511-5188
α-helix522-5298
Chain C: 27 helices, 30 β-strands
ElementResiduesLengthSheet
β-strand8-15816
α-helix30-4718
β-strand53-59716
β-strand77-78216
β-strand84116
α-helix88-958
α-helix108-12114
β-strand129-135716
α-helix148-1569
β-strand162-164316
α-helix199-21517
α-helix218-2225
β-strand224-225216
α-helix242-2432
β-strand246-253817
β-strand257-2681217
β-strand277-278213
β-strand290-296712
β-strand305112
α-helix307-3093
β-strand310-312311
β-strand315-316218
β-strand319-320218
α-helix326-3305
β-strand340-341217
β-strand342119
β-strand345115
β-strand346120
α-helix353-3553
β-strand360-366717
α-helix372-38615
β-strand390120
β-strand392-395419
α-helix402-4032
β-strand404-407419
α-helix4091
β-strand410117
α-helix4111
β-strand419-421317
β-strand422-423219
β-strand430110
α-helix445-4473
α-helix448-46013
β-strand46219
β-strand466121
β-strand473121
α-helix485-49915
α-helix507-5093
α-helix510-5156
α-helix520-53617
α-helix550-5523
α-helix597-6048
α-helix611-62515
α-helix629-64820
α-helix653-66816
α-helix672-68110
α-helix700-7045

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
>7Z88_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
>7Z88_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
>7Z88_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
>7Z88_4 DNA (26-MER) (chains D)
CCCGCTGCCGATTCCGCTGGAACATT
Sequence of entity 5 (E), FASTA
>7Z88_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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