7OTM: DNA-PKcs

Cryo-EM structure of DNA-PKcs in complex with NU7441. Determined by electron microscopy at 3.33 Å resolution. Released 12 Jan 2022.

Method
Electron microscopy
Resolution
3.33 Å
Organism
Homo sapiens
Chains
1
Atoms
29,040
Mol. weight
471.79 kDa
Ligands
2R4
Released
12 Jan 2022

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

Secondary structure: helices and β-sheets

7OTM contains 227 α-helices and 25 β-strands across 1 chain. 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: 227 helices, 25 β-strands

ElementResiduesLengthSheet
α-helix12-2211
α-helix34-4411
α-helix50-534
α-helix54-7017
α-helix79-9618
α-helix104-11411
α-helix115-1173
α-helix129-14517
α-helix154-1629
α-helix174-1774
α-helix179-1846
α-helix192-20615
α-helix218-23114
α-helix243-25412
α-helix258-2614
α-helix267-27711
α-helix285-2884
α-helix290-30213
α-helix309-32921
α-helix335-35016
α-helix359-36810
α-helix370-3767
α-helix381-39212
α-helix393-3975
α-helix407-4093
α-helix410-42112
α-helix432-44413
α-helix454-46815
α-helix472-4743
α-helix475-4806
α-helix481-49212
α-helix494-4952
α-helix525-53511
α-helix540-5445
α-helix560-57819
β-strand583-58531
β-strand612-61431
α-helix617-63317
α-helix645-65915
α-helix664-67815
α-helix698-71720
α-helix718-7203
α-helix725-7339
α-helix738-7414
α-helix745-75814
α-helix763-77917
α-helix782-7854
α-helix786-7883
α-helix789-7924
α-helix793-7964
α-helix797-8015
α-helix848-86114
α-helix867-8715
α-helix873-8764
α-helix881-8833
β-strand893-89532
α-helix9031
β-strand904-90632
α-helix907-9104
α-helix911-92010
α-helix926-94520
α-helix959-97315
α-helix978-99518
α-helix1003-10053
α-helix1008-10158
α-helix1024-104320
α-helix1046-10494
α-helix1056-106712
α-helix1073-108513
α-helix1093-111321
α-helix1114-11163
α-helix1123-114523
β-strand114913
α-helix1152-11543
β-strand116313
α-helix1165-117410
α-helix1181-119414
α-helix1195-11973
α-helix1204-121411
α-helix1217-12259
α-helix1234-12374
α-helix1252-127221
α-helix1278-12814
α-helix1289-12979
α-helix1324-13263
α-helix1327-135024
α-helix1355-13606
α-helix1365-137713
α-helix1379-13824
α-helix1391-140818
α-helix1412-14209
α-helix1425-143410
α-helix1442-146120
α-helix1464-14674
α-helix1477-14826
α-helix1483-14886
α-helix1507-151913
α-helix1525-15328
β-strand153714
β-strand154015
β-strand155115
β-strand155414
α-helix1555-15628
α-helix1564-157310
α-helix1575-158410
α-helix1592-160615
α-helix1612-162514
α-helix1626-16327
α-helix1639-165517
α-helix1668-167912
α-helix1686-16927
α-helix1693-16986
α-helix1707-172115
α-helix1734-175320
α-helix1756-176611
α-helix1775-178511
α-helix1791-180515
α-helix1813-18197
α-helix1820-18245
α-helix1825-18284
α-helix1835-185218
α-helix1863-188119
α-helix1886-18894
α-helix1911-192010
α-helix1935-195521
α-helix2094-210613
α-helix2124-213411
α-helix2140-215213
α-helix2161-217111
α-helix2184-219512
α-helix2206-222116
α-helix2228-224417
α-helix2255-22606
α-helix2268-22703
α-helix2271-228212
α-helix2297-23048
α-helix2305-23084
α-helix2313-233220
α-helix2339-235113
α-helix2358-236811
α-helix2372-23776
α-helix2379-23857
α-helix2392-240312
α-helix2413-24175
α-helix2420-24245
α-helix2429-244214
α-helix2443-24453
α-helix2448-24558
α-helix2458-24614
α-helix2470-248314
α-helix2497-250812
α-helix2509-25113
α-helix2515-252511
α-helix2535-25417
α-helix2543-25453
α-helix2558-25636
α-helix2564-25685
α-helix2788-279811
α-helix2802-281918
α-helix2820-28223
α-helix2826-284520
α-helix2852-286312
α-helix2868-28703
α-helix2873-288210
α-helix2886-289813
α-helix2918-293316
α-helix2936-29427
α-helix2943-29475
α-helix2952-296110
α-helix2965-297612
α-helix2985-29873
α-helix2988-300417
α-helix3008-30125
α-helix3027-30304
α-helix3041-305313
α-helix3060-307011
α-helix3075-30806
α-helix3083-309311
α-helix3096-311520
α-helix3122-31309
α-helix3133-314513
α-helix3154-316613
α-helix3176-319318
α-helix3194-31963
α-helix3231-324818
α-helix3254-32618
α-helix3272-328615
α-helix3291-330616
α-helix3319-33235
α-helix3324-334320
α-helix3346-33516
α-helix3354-33563
α-helix3358-33636
α-helix3370-339324
α-helix3407-342822
α-helix3442-345413
α-helix3459-34624
α-helix3466-34716
α-helix3476-34783
α-helix3481-34888
α-helix3499-35024
α-helix3515-352410
α-helix3530-35378
α-helix3549-356214
α-helix3567-35759
α-helix3581-359313
α-helix3606-36083
α-helix3609-36146
α-helix3627-36326
α-helix3633-36375
α-helix3640-36434
α-helix3658-367013
α-helix3687-36893
β-strand370016
α-helix3716-37172
β-strand371816
β-strand3719-372247
β-strand3727-372828
β-strand3736-373728
β-strand3739-374247
β-strand3746-374947
β-strand375218
α-helix3759-377719
α-helix3780-37834
β-strand379319
β-strand3797110
β-strand3800110
β-strand380319
β-strand3809-3811311
α-helix3812-38198
α-helix3822-38298
α-helix3835-384612
α-helix3854-38618
α-helix3864-387714
α-helix3883-38897
α-helix3894-391825
α-helix3925-39273
β-strand3928-3931411
β-strand3937-3939311
α-helix3948-39514
α-helix3965-39695
α-helix3979-399315
α-helix3995-400612
α-helix4013-40219
α-helix4041-40499
α-helix4050-40523
α-helix4056-406712
α-helix4074-40829
α-helix4100-411213
α-helix4114-41174
α-helix4122-41243
α-helix6003-601513

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA-dependent protein kinase catalytic subunit,DNA-PKcsAprotein4148Homo sapiensP78527
Sequence of entity 1 (A), FASTA
>7OTM_1 DNA-dependent protein kinase catalytic subunit,DNA-PKcs (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
ARGSKDHNIRAQEPESGLSEETQVKCLMDQATDPNILGRTWEGWEPWMXXXXXXXXXXXX
XXXXXXXX

Ligands and cofactors

IDNameFormulaCopies
2R48-(dibenzo[b,d]thiophen-4-yl)-2-(morpholin-4-yl)-4H-chromen-4-oneC25 H19 N O3 S1

Primary citation

Structural insights into inhibitor regulation of the DNA repair protein DNA-PKcs. Liang, S., Thomas, S.E., Chaplin, A.K. et al. Nature (2022) 601:643-648. DOI 10.1038/s41586-021-04274-9 · PubMed

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

Browse structure collections

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