Structure of PDB 8ezb Chain C

Receptor sequence
>8ezbC (length=3724) Species: 9606 (Homo sapiens) [Search protein sequence]
AGVRCSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQT
SLVFSRDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSV
EIKNTCTSVYTKDRAAKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSK
FYGELALKKKIPDTVLEKVYELLGLLGEVHPSEMINNAENLFRAFLGELK
TQMTSAVREPKLPVLAGCLKGLSSLLCNFTKSMEEDPQTSREIFNFVLKA
IRPQIDLKRYAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKWCAHTN
VELKKAALSALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIIRNVDSN
NKELSIAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTQTDTGDD
RVYQMPSFLQSVASVLLYLDTVPEVYTPVLEHLVVMQIDSFPQYSPKMQL
VCCRAIVKVFLALAAKGPVLRNCISTVVHQGLIRICSKPVVLPTYKDYVD
LFRHLLSSDQMMDSSESLNHLLYDEFVKSVLKIVEKLDLTLEIAANLHPA
KPKDFSAFINLVEFCREILPEKQAEFFEPWVYSFSYELILQSTRLPLISG
FYKLLSITVRNAKKIKYFEGVPEKYSCFALFVKFGKEVAVKMKQYKDELL
ASCLTFLLSLPHNIIELDVRAYVPALQMAFKLGLSYTPLAEVGLNALEEW
SIYIDRHVMQPYYKDILPCLDGYLKTSALAISLEEIRIRVVQMLGSLGGQ
INKNLLTVTSSDEMMKSYVAWDREKRLSFAVPFREMKPVIFLDVFLPRVT
ELALTASDRQTKVAACELLHSMVMFMLGKATQMPEGGQGAPPMYQLYKRT
FPVLLRLACDVDQVTRQLYEPLVMQLIHWFTNNKKFESQDTVALLEAILD
GIVDPVDSTLRDFCGRCIREFLKWSIKQITPQQQEKSPVNTKSLFKRLYS
LALHPNAFKRLGASLAFNNIYREFREEESLVEQFVFEALVIYMESLALAH
ADEKSLGTIQQCCDAIDHLCRIIEKKHVSLNKAKKRRLPRGFPPSASLCL
LDLVKWLLAHCGRPQTECRHKSIELFYKFVPLLPGNRSPNLWLKDVLKEE
GVSFLINTFEGGGCGQPSGILAQPTLLYSLQATLCWLDLLLAALECYNTF
IGERTVGALQVLGTEAQSSLLKAVAFFLESIAMHDIIAAEKCFGTGAAGN
RTSPQEGERYNYSKCTVVVRIMEFTTTLLNTSPEGWKLLKKDLCNTHLMR
VLVQTLCEPASIGFNIGDVQVMAHLPDVCVNLMKALKMSPYKDILETHLR
EKITAQSIEELCAVNLYGPDAQVDRSRLAAVVSACKQLHRAGLLHNILPS
QSTDLHHSVGTELLSLVYKGIAPGDERQCLPSLDLSCKQLASGLLELAFA
FGGLCERLVSLLLNPAVLSTSVIHFSHGEYFYSLFSETINTELLKNLDLA
VLELMQSSVDNTKMVSAVLNGMLDQSFRERANQKHQGLKLATTILQHWKK
CDSWWAKDSPLETKMAVLALLAKILQIDSSVSFNTSHGSFPEVFTTYISL
LADTKLDLHLKGQAVTLLPFFTSLTGGSLEELRRVLEQLIVAHFPMQSRE
FPPGTPRFNNYVDCMKKFLDALELSQSPMLLELMTEVLCREQQHVMEELF
QSSFRRIARRGSCVTQVGLLESVYEMFRKDDPRLSFTRQSFVDRSLLTLL
WHCSLDALREFFSTIVVDAIDVLKSRFTKLNESTFDTQITKKMGYYKILD
VMYSRLPKDDVHAKESKINQVFHGSCITEGNELTKTLIKLCYDAFTENMA
GENQLLERRRLYHCAAYNCAISVICCVFNELKFYQGFLFSEKPEKNLLIF
ENLIDLKRRYNFPVEVMDELNRHECMAPLTALVKHMHRSLPRDLPSWMKF
LHGKLGNPIVPLNIRLFLAKLVINTEEVFRPYAKHWLSPLLQLAASENNG
GEGIHYMVVEIVATILSWTGLATPTGVPKDEVLANRLLNFLMKHVFHPKR
AVFRHNLEIIKTLVECWKDCLSIPYRLIFEKFSGKDPNSKDNSVGIQLLG
IVMANDLPPYDPQCGIQSSEYFQALVNNMSFVRYKEVYAAAAEVLGLILR
YVMERKNILEESLCELVAKQLKQHQNTMEDKFIVCLNKVTKSFPPLADRF
MNAVFFLLPKFHGVLKTLCLEVVLCRVEGMTELYFQLKSKDFVQVMRHRD
DERQKVCLDIIYKMMPKLKPVELRELLNPVVEFVSHPSTTCREQMYNILM
WIHDNYRDPESETDNDSQEIFKLAKDVLIQGLIDENPGLQLIIRNFWSHE
TRLPSNTLDRLLALNSLYSPKIEVHFLSLATNFLLEMTSMSPDYPNPMFE
HPLSECEFQEYTIDSDWRFRSTVLTPMFVETQASQGPVAGQIRATQQQHD
FTLTQTQVVLYRSYRHGDLPDIQIKHSSLITPLQAVAQRDPIIAKQLFSS
LFSGILKEMDKFKTLSEKNNITQKLLQDFNRFLNTTFSFFPPFVSCIQDI
SCQHAALLSLDPAAVSAGCLASLQQPVGIRLLEEALLRLLPALPPDVLRW
VELAKLYRSIGEYDVLRGIFTSEIGTKQITQSALLAEARSDYSEAAKQYD
EALNKQDWVDGEPTEAEKDFWELASLDCYNHLAEWKSLEYCSTASIDSEN
PPDLNKIWSEPFYQETYLPYMIRSKLKLLLQGEADQSLLTFIDKAMHGEL
QKAILELHYSQELSLLYLLQDDVDRAKYYIQNGIQSFMQNYSSIDVLLHQ
SRLTKLQSVQALTEIQEFISFISKQGNLSSQVPLKRLLNTWTNRYPDAKM
DPMNIWDDIITNRCFFLSKIEEKLTEDISSLIRSCKFSMKMKMIDSARKQ
NNFSLAMKLLKELHKESKTRDDWLVSWVQSYCRLSHCRSRSQGCSEQVLT
VLKTVSLLDENNVSSYLSKNILAFRDQNILLGTTYRIIANALSSEPACLA
EIEEDKARRILELSGSSSEDSEKVIAGLYQRAFQHLSEAVQAAEEEAQPP
PAAGVIDAYMTLADFCDQQLRKEEENASVIDSAELQAYPALVVEKMLKAL
KLNSNEARLKFPRLLQIIERYPEETLSLMTKEISSVPCWQFISWISHMVA
LLDKDQAVAVQHSVEEITDNYPQAIVYPFIISSESYSFKDTSTGHKNKEF
VARIKSKLDQGGVIQDFINALDQLSNPELLFKDWSNDVRAELAKTPVNKK
NIEKMYERMYAALGDPKAPGLGAFRRKFIQTFGKEFDKHFGKGGSKLLRM
KLSDFNDITNMLLLKMNKDSKPPGNLKECSPWMSDFKVEFLRNELEIPGQ
YDGRGKPLPEYHVRIAGFDERVTVMASLRRPKRIIIRGHDEREHPFLVKG
GEDLRQDQRVEQLFQVMNGILAQDSACSQRALQLRTYSVVPMTSRLGLIE
WLENTVTLKDLLLNTMSQEEKAAYLSDPRAPPCEYKDWLTKMSGKHDVGA
YMLMYKGANRTETVTSFRKRESKVPADLLKRAFVRMSTSPEAFLALRSHF
ASSHALICISHWILGIGDRHLNNFMVAMETGGVIGIDFGHAFGSATQFLP
VPELMPFRLTRQFINLMLPMKETGLMYSIMVHALRAFRSDPGLLTNTMDV
FVKEPSFDWKNFEQKMLKKGGSWIQEINVAEKNWYPRQKICYAKRKLAGA
NPAVITCDELLLGHEKAPAFRDYVAVARGSKDHNIRAQEPESGLSEETQV
KCLMDQATDPNILGRTWEGWEPWM
3D structure
PDB8ezb Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ.
ChainC
Resolution8.9 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 dna C R264 Y265 H303 T304 N305 R259 Y260 H298 T299 N300
BS02 dna C K263 K357 D404 Y408 K258 K352 D399 Y403
BS03 MG C H3924 N3927 D3941 H3520 N3523 D3537
BS04 ATP C S3731 K3753 W3805 T3811 N3926 M3929 D3941 S3327 K3349 W3401 T3407 N3522 M3525 D3537
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
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Cellular Component
External links
PDB RCSB:8ezb, PDBe:8ezb, PDBj:8ezb
PDBsum8ezb
PubMed37256947
UniProtP78527|PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit (Gene Name=PRKDC)

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