Structure of PDB 7sud Chain A Binding Site BS03

Receptor Information
>7sud Chain A (length=3740) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GVRCSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQTS
LVFSRDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSVE
IKNTCTSVYTKDRAAKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSKF
YGELALKKKIPDTVLEKVYELLGLLGEVHPSEMINNAENLFRAFLGELKT
QMTSAVREPKLPVLAGCLKGLSSLLCNFTKSMEEDPQTSREIFNFVLKAI
RPQIDLKRYAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKWCAHTNV
ELKKAALSALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIIRNVDSNN
KELSIAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTQTDTGDDR
VYQMPSFLQSVASVLLYLDTVPEVYTPVLEHLVVMQIDSFPQYSPKMQLV
CCRAIVKVFLALAAKGPVLRNCISTVVHQGLIRICSKPVVWKVPTYKDYV
DLFRHLLSSDQMMDSILAESLNHLLYDEFVKSVLKIVEKLDLTLEIQAAN
LHPAKPKDFSAFINLVEFCREILPEKQAEFFEPWVYSFSYELILQSTRLP
LISGFYKLLSITVRNAKKIKYFEGVPEKYSCFALFVKFGKEVAVKMKQYK
DELLASCLTFLLSLPHNIIELDVRAYVPALQMAFKLGLSYTPLAEVGLNA
LEEWSIYIDRHVMQPYYKDILPCLDGYLKTTKNNWEVSALSRAAQKGAIS
LEEIRIRVVQMLGSLGGQINKNLLTVTSSDEMMKSYVAWDREKRLSFAVP
FREMKPVIFLDVFLPRVTELALTASDRQTKVAACELLHSMVMFMLGKATQ
MPEGGQGAPPMYQLYKRTFPVLLRLACDVDQVTRQLYEPLVMQLIHWFTN
NKKFESQDTVALLEAILDGIVDPVDSTLRDFCGRCIREFLKWSIKQITPQ
QQEKSPVNTKSLFKRLYSLALHPNAFKRLGASLAFNNIYREFREEESLVE
QFVFEALVIYMESLALAHADEKSLGTIQQCCDAIDHLCRIIEKKHVSLNK
AKKRRLPRGFPPSASLCLLDLVKWLLAHCGRPQTECRHKSIELFYKFVPL
LPGNRSPNLWLKDVLKEEGVSFLINTFEGGGCGQPSGILAQPTLLYLRGP
FSLQATLCWLDLLLAALECYNTFIGERTVGALQVLGTEAQSSLLKAVAFF
LESIAMHDIIAAEKCNRTSPQEGERYNYSKCTVVVRIMEFTTTLLNTSPE
GWKLLKKDLCNTHLMRVLVQTLCEPASIGFNIGDVQVMAHLPDVCVNLMK
ALKMSPYKDILETHLREKITAQSIEELCAVNLYGPDAQVDRSRLAAVVSA
CKQLHRAGLLHNILPSQSTDLHHSVGTELLSLVYKGIAPGQCLPSLDLSC
KQLASGLLELAFAFGGLCERLVSLLLNPAVLSTAVIHFSHGEYFYSLFSE
TINTELLKNLDLAVLELMQSSVDNTKMVSAVLNGMLDQSFRERANQKHQG
LKLATTILQHWKKCDSWWAKDSPLETKMAVLALLAKILQIDSSVSFNTSH
GSFPEVFTTYISLLADTKLDLHLKGQAVTLLPFFTSLTGGSLEELRRVLE
QLIVAHFPMQSREFPPGTPRFNNYVDCMKKFLDALELSQSPMLLELMTEV
LCREQQHVMEELFQSSFRRIARRGSCVTQVGLLESVYEMFRKDDPRLSFT
RQSFVDRSLLTLLWHCSLDALREFFSTIVVDAIDVLKSRFTKLNESTFDT
QITKKMGYYKILDVMYSRLPKDDVHAKESKINQVFHGSCITEGNELTKTL
IKLCYDAFTENMAGENQLLERRRLYHCAAYNCAISVICCVFNELKFYQGF
LFSEKPEKNLLIFENLIDLKRRYNFPVEVEVPMERKKKYIEIRKEAREAA
NGDSDGPSYMDELNRHECMAPLTALVKHMHRSLLPSWMKFLHGKLGNPIV
PLNIRLFLAKLVINTEEVFRPYAKHWLSPLLQLAASENNGGEGIHYMVVE
IVATILSWTGLATPTGVPKDEVLANRLLNFLMKHVFHPKRAVFRHNLEII
KTLVECWKDCLSIPYRLIFEKFSGKDPNSKDNSVGIQLLGIVMANDLPPY
DPQCGIQSSEYFQALVNNMSFVRYKEVYAAAAEVLGLILRYVMERKNILE
ESLCELVAKQLKQHQNTMEDKFIVCLNKVTKSFPPLADRFMNAVFFLLPK
FHGVLKTLCLEVVLCRVEGMTELYFQLKSKDFVQVMRHRDDERQKVCLDI
IYKMMPKLKPVELRELLNPVVEFVSHPSTTCREQMYNILMWIHDNYRDPE
SETDNDSQEIFKLAKDVLIQGLIDENPGLQLIIRNFWSHETRLPSNTLDR
LLALNSLYSPKIEVHFLSLATNFLLEMTSMSPDYPNPMFEHPLSECEFQE
YTIDSDWRFRSTVLTPMFVETQASQGQIRATQQQHDFTLTQVVLYRSYRH
GDLPDIQIKHSSLITPLQAVAQRDPIIAKQLFSSLFSGILKEMDKFKTLS
EKNNITQKLLQDFNRFLNTTFSFFPPFVSCIQDISCQHAALLSLDPAAVS
AGCLASLQQPVGIRLLEEALLRPPDVLRWVELAKLYRSIGEYDVLRGIFT
SEIGTKQITQSALLAEARSDYSEAAKQYDEALNKQDWVDGEPTEAEKDFW
ELASLDCYNHLAEWKSLEYCSTASIDSENPPDLNKIWSEPFYQETYLPYM
IRSKLKLLLQGEADQSLLTFIDKAMHGELQKAILELHYSQELSLLYLLQD
DVDRAKYYIQNGIQSFMQNYSSIDVLLHQSRLTKLQSVQALTEIQEFISF
ISKQGNLSSQVPLKRLLNTWTNRYPDAKMDPMNIWDDIITNRCFFLSKIE
EKLTDISSLIRSCKFSMKMKMIDSARKQNNFSLAMKLLKELHKESKTRDD
WLVSWVQSYCRLSHCRSRSQGCSEQVLTVLKTVSLLDENNVSSYLSKNIL
AFRDQNILLGTTYRIIANALSSEPACLAEIEEDKARRILELSGSSSEDSE
KVIAGLYQRAFQHLSEAVQAAEEAAGVIDAYMTLADFCDQQLRKEEENAE
LQAYPALVVEKMLKALKLNSNEARLKFPRLLQIIERYPEETLSLMTKEIS
SVPCWQFISWISHMVALLDKDQAVAVQHSVEEITDNYPQAIVYPFIISSE
SYSFKDTSTGHKNKEFVARIKSKLDQGGVIQDFINALDQLSNPELLFKDW
SNDVRAELAKTPVNKKNIEKMYERMYAALGDPKAPGLGAFRRKFIQTFGK
EFDKHFGKGGSKLLRMKLSDFNDITNMLLLKMNKDSKPPGNLKECSPWMS
DFKVEFLRNELEIPGQYDGRGKPLPEYHVRIAGFDERVTVMASLRRPKRI
IIRGHDEREHPFLVKGGEDLRQDQRVEQLFQVMNGILAQDSACSQRALQL
RTYSVVPMTSRLGLIEWLENTVTLKDLLLNTMSQEEKAAYLSDPRAPPCE
YKDWLTKMSGKHDVGAYMLMYKGANRTETVTSFRKRESKVPADLLKRAFV
RMSTSPEAFLALRSHFASSHALICISHWILGIGDRHLNNFMVAMETGGVI
GIDFGHAFGSATQFLPVPELMPFRLTRQFINLMLPMKETGLMYSIMVHAL
RAFRSDPGLLTNTMDVFVKEPSFDWKNFEQKMLKKGGSWIQEINVAEKNW
YPRQKICYAKRKLAGANPAVITCDELLLGHEKAPAFRDYVAVARGSKDHN
IRAQEPESGLSEETQVKCLMDQATDPNILGRTWEGWEPWM
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain7sud Chain A Residue 4202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7sud Autophosphorylation transforms DNA-PK from protecting to processing DNA ends.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		S3731 L3751 K3753 E3804 W3805 L3806 M3929 D3941
Binding residue
(residue number reindexed from 1)		S3343 L3363 K3365 E3416 W3417 L3418 M3541 D3553
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003690 double-stranded DNA binding
GO:0003723 RNA binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004677 DNA-dependent protein kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0019899 enzyme binding
GO:0019904 protein domain specific binding
GO:0034511 U3 snoRNA binding
GO:0035979 histone H2AXS139 kinase activity
GO:0044024 histone H2AS1 kinase activity
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0000460 maturation of 5.8S rRNA
GO:0000723 telomere maintenance
GO:0001756 somitogenesis
GO:0001933 negative regulation of protein phosphorylation
GO:0002218 activation of innate immune response
GO:0002326 B cell lineage commitment
GO:0002327 immature B cell differentiation
GO:0002328 pro-B cell differentiation
GO:0002360 T cell lineage commitment
GO:0006281 DNA repair
GO:0006302 double-strand break repair
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006310 DNA recombination
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0006974 DNA damage response
GO:0007420 brain development
GO:0007507 heart development
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
GO:0010212 response to ionizing radiation
GO:0010332 response to gamma radiation
GO:0016233 telomere capping
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0018107 peptidyl-threonine phosphorylation
GO:0019219 regulation of nucleobase-containing compound metabolic process
GO:0030098 lymphocyte differentiation
GO:0031571 mitotic G1 DNA damage checkpoint signaling
GO:0031648 protein destabilization
GO:0032869 cellular response to insulin stimulus
GO:0033077 T cell differentiation in thymus
GO:0033151 V(D)J recombination
GO:0033152 immunoglobulin V(D)J recombination
GO:0033153 T cell receptor V(D)J recombination
GO:0034462 small-subunit processome assembly
GO:0035234 ectopic germ cell programmed cell death
GO:0036211 protein modification process
GO:0042254 ribosome biogenesis
GO:0042752 regulation of circadian rhythm
GO:0043065 positive regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0045087 innate immune response
GO:0045621 positive regulation of lymphocyte differentiation
GO:0045648 positive regulation of erythrocyte differentiation
GO:0045727 positive regulation of translation
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0048511 rhythmic process
GO:0048660 regulation of smooth muscle cell proliferation
GO:0050678 regulation of epithelial cell proliferation
GO:0080135 regulation of cellular response to stress
GO:0097681 double-strand break repair via alternative nonhomologous end joining
GO:0160049 negative regulation of cGAS/STING signaling pathway
GO:1902036 regulation of hematopoietic stem cell differentiation
GO:1905221 positive regulation of platelet formation
GO:2001034 positive regulation of double-strand break repair via nonhomologous end joining
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription regulator complex
GO:0005730 nucleolus
GO:0005829 cytosol
GO:0005958 DNA-dependent protein kinase-DNA ligase 4 complex
GO:0016020 membrane
GO:0032040 small-subunit processome
GO:0032991 protein-containing complex
GO:0032993 protein-DNA complex
GO:0070418 DNA-dependent protein kinase complex
GO:0070419 nonhomologous end joining complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7sud, PDBe:7sud, PDBj:7sud
PDBsum7sud
PubMed34936881
UniProtP78527|PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit (Gene Name=PRKDC)

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