Structure of PDB 5y3r Chain C

Receptor sequence
>5y3rC (length=3636) Species: 9606 (Homo sapiens) [Search protein sequence]
CSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQTSLVF
SRDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSVEIKN
TCTSVYTKDRAAKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSKFYGE
LALKKKIPDTVLEKVYELLGLLGEVHPSEMINNAENLFRAFLGELKTQMT
SAVREPKLPVLAGCLKGLSSLLCNFTKSMEEDPQTSREIFNFVLKAIRPQ
IDLKRYAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKWCAHTNVELK
KAALSALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIIRNVDSNNKEL
SIAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTQTDTGDDRVYQ
MPSFLQSVASVLLYLDTVPEVYTPVLEHLVVMQIDSFPQYSPKMQLVCCR
AIVKVFLALAAKGPVLRNCISTVVHQGLIRICSKPVVLKDYVDLFRHLLS
SDQMMDSILADEAFFSVNSSSESLNHLLYDEFVKSVLKIVEKLDLTLEIQ
TVGEQENGDEAPGVWMIPTSDPAANLHPAKPKDFSAFINLVEFCREILPE
KQAEFFEPWVYSFSYELILQSTRLPLISGFYKLLSITVRNAKKIKYKYSC
FALFVKFGKEVAVKMKQYKDELLASCLTFLLSLPHNIIELDVRAYVPALQ
MAFKLGLSYTPLAEVGLNALEEWSIYIDRHVMQPYYKDILPCLDGYLKTS
ALSDETISLEEIRIRVVQMLGSLGGQINKNLLTVTSSDEMMKSYVAWDRE
KRLSFAVPFREMKPVIFLDVFLPRVTELALTASDRQTKVAACELLHSMVM
FMLGKATQMPEGGQGAPPMYQLYKRTFPVLLRLACDVDQVTRQLYEPLVM
QLIHWFTNNKKFESQDTVALLEAILDGIVDPVDSTLRDFCGRCIREFLKW
SIKQITPQQQEKSPVNTKSLFKRLYSLALHPNAFKRLGASLAFNNIYREF
REEESLVEQFVFEALVIYMESLALAHADEKSLGTIQQCCDAIDHLCRIIE
KKHVSLNKAKKRRLPRGFPPSASLCLLDLVKWLLAHCGRPQKEEGVSFLI
NTFEGGGCGQPSGILAQPTLLYLRGPFSLQATLCWLDLLLAALECYNTFI
GERTVGALQVLGTEAQSSLLKAVAFFLESIAMHDIIASPQEGERYNYSKC
TVVVRIMEFTTTLLNTSPEGWKLLKKDLCNTHLMRVLVQTLCEPASIGFN
IGDVQVMAHLPDVCVNLMKALKMSPYKDILETHLREKITAQSIEELCAVN
LYGPDAQVDRSRLAAVVSACKQLHRAGLLHNILPSQSTDLHHSVGTELLS
LVYKGIAPGDERQCLPSLDLSCKQLASGLLELAFAFGGLCEGSVIHFSHG
EYFYSLFSETINTELLKNLDLAVLELMQSSVDNTKMVSAVLNGMLDQSFR
ERADSWWAKDSPLETKMAVLALLAKILQIDSSVFTTYISLLADTKLDLHL
KGQAVTLLPFFTSLTGGSLEELRRVLEQLIVAHFPMQSREFPPGTPRFNN
YVDCMKKFLDALELSQSPMLLELMTLESVYEMFRKDDPRLSFTRQSFVDR
TKLNESTFDTQITKKMGYYKILDVMYSRLPKDDVHAKESKINQVFHGSCI
TEGNELTKTLIKLCYDAFTENMAGENQLLERRRLYHCAAYNCAISVICCV
FNELKFYQGFLFSEKPEKNLLIFENLIDLKRRYNFPVEVEVPMERKKKYI
EIRKEAREAANGDSDGPSYMSSLSYLADSTLSEEMSQFDFSTGVQSYSYS
SQDPRPATGRFRRREQRDPTVHDDVLELEMDELNRHECMAPLTALVKHMH
RSLGPPQGEEDSVPRDLPSWMKFLHGKLGNPIVPLNIRLFLAKLVINTEE
VFRPYAKHWLSPLLQLAASENNGGEGIHYMVVEIVATILSWTGLATPTGV
PKDEVLANRLLNFLMKHVFHPKRAVFRHNLEIIKTLVECWKDCLSIPYRL
IFEKFSGKDPNSKDNSVGIQLLGIVMANDLPPYDPQCGIQSSEYFQALVN
NMSFVRYKEVYAAAAEVLGLILRYVMERKNILEESLCELVAKQLKQHQNT
MEDKFIVCLNKVTKSFPPLADRFMNAVFFLLPKFHGVLKTLCLEVVLCRV
EGMTELYFQLKSKDFVQVMRHRDDERQKVCLDIIYKMMPKLKPVELRELL
NPVVEFVSHPSTTCREQMYNILMWIHDNYRDPESETDNDSQEIFKLAKDV
LIQGLIDENPGLQLIIRNFWSHETRLPSNTLDRLLALNSLYSPKIEVHFL
SLATNFLLEMTSMSPDYPNPMSYRHGDLPDIQIKHSSLITPLQAVAQRDP
IIAKQLFSSLFSGILKEMDKFKTLSEKNNITQKLLQDFNRFLNTTFSFFP
PFVSCIQDISCQHAALLSLDPAAVSAGCLASLQQPVGIRLLEEALLRLLP
AELPAKRVRGKARLPPDVLRWVELAKLYRSIGEYDVLRGIFTSEIGTKQI
TQSALLAEARSDYSEAAKQYDEALNKQDWVDGEPTEAEKDFWELASLDCY
NHLAEWKSLEYCSTASIDSENPPDLNKIWSEPFYQETYLPYMIRSKLKLL
LQGEADQSLLTFIDKAMHGELQKAILELHYSQELSLLYLLQDDVDRAKYY
IQNGIQSFMQNYSSIDVLLHQSRLTKLQSVQALTEIQEFISFISKQGNLS
SQVPLKRLLNTWTNRYPDAKMDPMNIWDDIITNRCFFLSKIEEKLTPISS
LIRSCKFSMKMKMIDSARKQNNFSLAMKLLKELHKESKTRDDWLVSWVQS
YCRLSHCRSRSQGCSEQVLTVLKTVSLLDENNVSSYLSKNILAFRDQNIL
LGTTYRIIANALSSEPACLAEIEEDKARRIVIAGLYQRAFQHLSEAVQAA
EEEAQPPSWSCGPAAGVIDAYMTLADFCDQQLRKEEENASVIDSAELQAY
PALVVEKMLKALKLNSNEARLKFPRLLQIIERYPEETLSLMTKEISSVPC
WQFISWISHMVALLDKDQAVAVQHSVEEITDNYPQAIVYPFIISSESYSF
KDTSTGHKNKEFVARIKSKLDQGGVIQDFINALDQLSNPELLFKDWSNDV
RAELAKTPVNKKNIEKMYERMYAALGDPKAPGLGAFRRKFIQTFGKEFDK
HFGKGGSKLLRMKLSDFNDITNMLLLKMNKDSKPPGNLKECSPWMSDFKV
EFLRNELEIPGQYDGRGKPLPEYHVRIAGFDERVTVMASLRRPKRIIIRG
HDEREHPFLVKGGEDLRQDQRVEQLFQVMNGILAQDSACSQRALQLRTYS
VVPMTSRLGLIEWLENTVTLKDLLLNTMSQEEKAAYLSDPRAPPCEYKDW
LTKMSGKHDVGAYMLMYKGANRTETVTSFRKRESKVPADLLKRAFVRMST
SPEAFLALRSHFASSHALICISHWILGIGDRHLNNFMVAMETGGVIGIDF
GHAFGSATQFLPVPELMPFRLTRQFINLMLPMKETGLMYSIMVHALRAFR
SDPGLLTNTMDVFVKEPSFDWKNFEQKMLKKGGSWIQEINVAEKNWYPRQ
KICYAKRKLAGANPAVITCDELLLGHEKAPAFRDYVAVARGSKDHNIRAQ
EPESGLSEETQVKCLMDQATDPNILGRTWEGWEPWM
3D structure
PDB5y3r Cryo-EM structure of human DNA-PK holoenzyme
ChainC
Resolution6.6 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 peptide C L2194 T2240 L1939 T1985
BS02 dna C C123 K124 I125 L128 T169 R2311 Y2312 K2313 C114 K115 I116 L119 T160 R2056 Y2057 K2058
BS03 dna C I260 D261 F2231 M2356 I251 D252 F1976 M2101
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:5y3r, PDBe:5y3r, PDBj:5y3r
PDBsum5y3r
PubMed28840859
UniProtP78527|PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit (Gene Name=PRKDC)

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