Structure of PDB 8eza Chain L
Receptor sequence
>8ezaL (length=3720) Species:
9606
(Homo sapiens) [
Search protein sequence
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AGVRCSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQT
SLVFSRDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSV
EIKNTCTSVYTKDRAAKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSK
FYGELALKKKIPDTVLEKVYELLGLLGEVHPSEMINNAENLFRAFLGELK
TQMTSAVREPKLPVLAGCLKGLSSLLCNFTKSMEEDPQTSREIFNFVLKA
IRPQIDLKRYAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKWCAHTN
VELKKAALSALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIIRNVDSN
NKELSIAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTQTDTGDD
RVYQMPSFLQSVASVLLYLDTVPEVYTPVLEHLVVMQIDSFPQYSPKMQL
VCCRAIVKVFLALAAKGPVLRNCISTVVHQGLIRICSKPVVLPTYKDYVD
LFRHLLSSDQMMDSSESLNHLLYDEFVKSVLKIVEKLDLTLEIAANLHPA
KPKDFSAFINLVEFCREILPEKQAEFFEPWVYSFSYELILQSTRLPLISG
FYKLLSITVRNAKKIKYFEGVPEKYSCFALFVKFGKEVAVKMKQYKDELL
ASCLTFLLSLPHNIIELDVRAYVPALQMAFKLGLSYTPLAEVGLNALEEW
SIYIDRHVMQPYYKDILPCLDGYLKTSALEVSALSRAAQKGFNKVVLKHL
KKTKEAISLEEIRIRVVQMLGSLGGQINKNLLTVTSSDEMMKSYVAWDRE
KRLSFAVPFREMKPVIFLDVFLPRVTELALTASDRQTKVAACELLHSMVM
FMLGKATQMPEGGQGAPPMYQLYKRTFPVLLRLACDVDQVTRQLYEPLVM
QLIHWFTNNKKFESQDTVALLEAILDGIVDPVDSTLRDFCGRCIREFLKW
SIKQITPQQQEKSPVNTKSLFKRLYSLALHPNAFKRLGASLAFNNIYREF
REEESLVEQFVFEALVIYMESLALAHADEKSLGTIQQCCDAIDHLCRIIE
KKHVSLNKAKKRRLPRGFPPSASLCLLDLVKWLLAHCGRPQTECRHKSIE
LFYKFVPLLPGNRSPNLWLKDVLKEEGVSFLINTFEGGGCGQPSGILAQP
TLLYSLQATLCWLDLLLAALECYNTFIGERTVGALQVLGTEAQSSLLKAV
AFFLESIAMHDIIAAEKSPQEGERYNYSKCTVVVRIMEFTTTLLNTSPEG
WKLLKKDLCNTHLMRVLVQTLCEPASIGFNIGDVQVMAHLPDVCVNLMKA
LKMSPYKDILETHLREKITAQSIEELCAVNLYGPDAQVDRSRLAAVVSAC
KQLHRAGLLHNILPSQSTDLHHSVGTELLSLVYKGIAPGDERQCLPSLDL
SCKQLASGLLELAFAFGGLCERLVSLLLNPAVLSTSVIHFSHGEYFYSLF
SETINTELLKNLDLAVLELMQSSVDNTKMVSAVLNGMLDQSFRERANQKH
QGLKLATTILQHWKKCDSWWAKDSPLETKMAVLALLAKILQIDSSVSFNT
SHGSFPEVFTTYISLLADTKLDLHLKGQAVTLLPFFTSLTGGSLEELRRV
LEQLIVAHFPMQSREFPPGTPRFNNYVDCMKKFLDALELSQSPMLLELMT
EVLCREQQHVMEELFQSSFRRIARRGSCVTQVGLLESVYEMFRKDDPRLS
FTRQSFVDRSLLTLLWHCSLDALREFFSTIVVDAIDVLKSRFTKLNESTF
DTQITKKMGYYKILDVMYSRLPKDDVHAKESKINQVFHGSCITEGNELTK
TLIKLCYDAFTENMAGENQLLERRRLYHCAAYNCAISVICCVFNELKFYQ
GFLFSEKPEKNLLIFENLIDLKRRYNFPVMDELNRHECMAPLTALVKHMH
RSLPRDLPSWMKFLHGKLGNPIVPLNIRLFLAKLVINTEEVFRPYAKHWL
SPLLQLAASENNGGEGIHYMVVEIVATILSWTGLATPTGVPKDEVLANRL
LNFLMKHVFHPKRAVFRHNLEIIKTLVECWKDCLSIPYRLIFEKFSGKDP
NSKDNSVGIQLLGIVMANDLPPYDPQCGIQSSEYFQALVNNMSFVRYKEV
YAAAAEVLGLILRYVMERKNILEESLCELVAKQLKQHQNTMEDKFIVCLN
KVTKSFPPLADRFMNAVFFLLPKFHGVLKTLCLEVVLCRVEGMTELYFQL
KSKDFVQVMRHRDDERQKVCLDIIYKMMPKLKPVELRELLNPVVEFVSHP
STTCREQMYNILMWIHDNYRDPESETDNDSQEIFKLAKDVLIQGLIDENP
GLQLIIRNFWSHETRLPSNTLDRLLALNSLYSPKIEVHFLSLATNFLLEM
TSMSPDYPNPMFEHPLSECEFQEYTIDSDWRFRSTVLTPMGRTDLLRLRR
RFMRDQEKLSLMYARKGVAEQKREKEIKSELKMKQDAQVVLYRSYRHGDL
PDIQIKHSSLITPLQAVAQRDPIIAKQLFSSLFSGILKEMDKFKTLSEKN
NITQKLLQDFNRFLNTTFSFFPPFVSCIQDISCQHAALLSLDPAAVSAGC
LASLQQPVGIRLLEEALLRLLPRLPPDVLRWVELAKLYRSIGEYDVLRGI
FTSEIGTKQITQSALLAEARSDYSEAAKQYDEALNKQDWVDGEPTEAEKD
FWELASLDCYNHLAEWKSLEYCSTASIDSENPPDLNKIWSEPFYQETYLP
YMIRSKLKLLLQGEADQSLLTFIDKAMHGELQKAILELHYSQELSLLYLL
QDDVDRAKYYIQNGIQSFMQNYSSIDVLLHQSRLTKLQSVQALTEIQEFI
SFISKQGNLSSQVPLKRLLNTWTNRYPDAKMDPMNIWDDIITNRCFFLSK
IEEKLTPISSLIRSCKFSMKMKMIDSARKQNNFSLAMKLLKELHKESKTR
DDWLVSWVQSYCRLSHCRSRSQGCSEQVLTVLKTVSLLDENNVSSYLSKN
ILAFRDQNILLGTTYRIIANALSSEPACLAEIEEDKARRILELSGSSSED
SEKVIAGLYQRAFQHLSEAVQAAEEEAAGVIDAYMTLADFCDQQLRKEEE
NASVIDSAELQAYPALVVEKMLKALKLNSNEARLKFPRLLQIIERYPEET
LSLMTKEISSVPCWQFISWISHMVALLDKDQAVAVQHSVEEITDNYPQAI
VYPFIISSESYSFKDTSTGHKNKEFVARIKSKLDQGGVIQDFINALDQLS
NPELLFKDWSNDVRAELAKTPVNKKNIEKMYERMYAALGDPKAPGLGAFR
RKFIQTFGKEFDKHFGKGGSKLLRMKLSDFNDITNMLLLKMNKDSKPPGN
LKECSPWMSDFKVEFLRNELEIPGQYDGRGKPLPEYHVRIAGFDERVTVM
ASLRRPKRIIIRGHDEREHPFLVKGGEDLRQDQRVEQLFQVMNGILAQDS
ACSQRALQLRTYSVVPMTSRLGLIEWLENTVTLKDLLLNTMSQEEKAAYL
SDPRAPPCEYKDWLTKMSGKHDVGAYMLMYKGANRTETVTSFRKRESKVP
ADLLKRAFVRMSTSPEAFLALRSHFASSHALICISHWILGIGDRHLNNFM
VAMETGGVIGIDFGHAFGSATQFLPVPELMPFRLTRQFINLMLPMKETGL
MYSIMVHALRAFRSDPGLLTNTMDVFVKNWYPRQKICYAKRKLAGANPAV
ITCDELLLGHEKAPAFRDYVAVARGSKDHNIRAQEPESGLSEETQVKCLM
DQATDPNILGRTWEGWEPWM
3D structure
PDB
8eza
Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ.
Chain
L
Resolution
4.39 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
L
P433 K578 K616 K618 D619
P428 K536 K551 K553 D554
BS02
dna
L
R264 R2228 A2229 R2730 F2732 M2733 Q2736 L2739 Y2743
R259 R2013 A2014 R2400 F2402 M2403 Q2406 L2409 Y2413
BS03
dna
L
R119 A121 D168 T169 R820 R2311 K2313 A2744
R114 A116 D163 T164 R736 R2096 K2098 A2414
BS04
ATP
L
S3731 P3735 L3751 K3753 E3804 W3805 M3929 I3940 D3941
S3352 P3356 L3372 K3374 E3425 W3426 M3550 I3561 D3562
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
View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB
RCSB:8eza
,
PDBe:8eza
,
PDBj:8eza
PDBsum
8eza
PubMed
37256947
UniProt
P78527
|PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit (Gene Name=PRKDC)
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