BioLiP

>8botF (length=3535) Species: 9606 (Homo sapiens) [Search protein sequence]

CSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQTSLVF
SRDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSVEIKN
TCTSVYTKDRAAKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSKFYGE
LALKKKIPDTVLEKVYELLGLLGEVHPSEMINNAENLFRAFLGELKTQMT
SAVREPKLPVLAGCLKGLSSLLCNFTKSMEEDPQTSREIFNFVLQIDLKR
YAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKWCAHTNVELKKAALS
ALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIINKELSIAIRGYGLFA
GPCKVINAKDVDFMYVELIQRCKQMFLTQDRVYQMPSFLQSVASVLLYLD
TVPEVYTPVLEHLVVMQIDSFPQYSPKMQLVCCRAIVKVFLALAAKGPVL
RNCISTVVHQGLIRICSKPVVLPWKVPTYKDYVDLFRHLLSSDQMMDSIL
ADSLNHLLYDEFVKSVLKIVEKLDLTLEIQANLHPAKPKDFSAFINLVEF
CREILPEKQAEFFEPWVYSFSYELILQSTRLPLISGFYKLLSITVRNAKK
IKYFEGDPEKYSCFALFVKFGKEVAVKMKQYKDELLASCLTFLLSLPHNI
IELDVRAYVPALQMAFKLGLSYTPLAEVGLNALEEWSIYIDRHVMQPYYK
DILPCLDGYLKTSFNKVVLKHLKKTKNLSLEEIRIRVVQMLGSLGGQINK
NLLMMKSYVAWDREKRLSFAVPFREMKPVIFLDVFLPRVTELALTASDRQ
TKVAACELLHSMVMFMLGKATQMPEGGQGAPPMYQLYKRTFPVLLRLACD
VDQVTRQLYEPLVMQLIHWFTNNKKFESQDTVALLEAILDGIVDPVDSTL
RDFCGRCIREFLKWSIKQITPQQQEKSPVNTKSLFKRLYSLALHPNAFKR
LGASLAFNNIYREFREEESLVEQFVFEALVIYMESLALAHADEKSLGTIQ
QCCDAIDHLCRIIEKKHVSLNKAKKRRLPRGFPPSASLCLLDLVKWLLAH
CGRPQTECRHKSIELFYKFVPLLPGNRSPNLWLKDVLKEEGVSFLINTFE
GGGCGQPSGILAQPTSLQATLCWLDLLLAALECYNTFIGERTVGALQVLG
TEAQSSLLKAVAFFLESIAMHDIIAAEKCFTSPQEGERYNYSKCTVVVRI
MEFTTTLLNTSPEGWKLLKKDLCNTHLMRVLVQTLCEPASIGFNIGDVQV
MAHLPDVCVNLMKALKMSPYKDILETHLREKITAQSIEELCAVNLYGPDA
QVDRSRLAAVVSACKQLHRAGLLHNILPSQSTDLHHSVGTELLSLVYKGI
ALDLSCKQLASGLLELAFAFGGLCERLVSLLLNPAVLSTVIHFSHGEYFY
SLFSETINTELLKNLDLAVLELMQSSVDNTKMVSAVLNGMLDQSFRERAN
QKHQGLKLATTILQHWKKCDSWWAKDSPLETKMAVLALLAKILQIDSSVS
FNTSHGSFPEVFTTYISLLADTKLDLHLKGQAVTLLPFFLEELRRVLEQL
IVAHFPMQSREFPPGTPRFNNYVDCMKKFLDALELSQSPMLLELMTEVLC
REQQHVMEELFQSSFRRIARRGSCVTQVGLLESVYEMFRTRQSFVDRSLL
TLLWHCSLDALREFFSTIVVDAIDVLKTFDTQITKKMGYYKILDVMYSRL
PNELTKTLIKLCYDAFTENLERRRLYHCAAYNCAISVICCVFNELKFYQR
HECMAPLTALVKHMHRSLRDLPSWMKFLHGKLGNPIVPLNIRLFLAKLVI
NTEEVFRPYAKHWLSPLLQLAASENGEGIHYMVVEIVATILSWTGLATPT
GVPKDEVLANRLLNFLMKHVFHPKRAVFRHNLEIIKTLVECWKDCLSIPY
RLIFEKFSGKDPNSKDNSVGIQLLGIVMANDLPPYDPQCGIQSSEYFQAL
VNNMSFVRYKEVYAAAAEVLGLILRYVMERKNILEESLCELVAKQLKQHQ
NTMEDKFIVCLNKVTKSFPPLADRFMNAVFFLLPKFHGVLKTLCLEVVLC
RVEGMTELYFQLKSKDFVQVMRHRDDERQKVCLDIIYKMMPKLKPVELRE
LLNPVVEFVSHPSTTCREQMYNILMWIHDNYRDTDNDSQEIFKLAKDVLI
QGLIDENPGLQLIIRNFWSHETRLPSNTLDRLLALNSLYSPKIEVHFLSL
ATNFLLEMTSMSPDYPNPMFEHPLSECEFQEYTIDSDWRFRSTVLTGRTD
LLRLRRRFMRDQEKLSLMYARKGVAEQKREKEIKSELKMKQDAQVVLYRS
YRHGDLPDIQIKHSSLITPLQAVAQRDPIIAKQLFSSLFSGILKEMDKFK
TLSEKNNITQKLLQDFNRFLNTTFSFFPPFVSCIQDISCQHAALLSLDPA
AVSAGCLASLQQPVGIRLLEEALLRLLLPPDVLRWVELAKLYRSIGEYDV
LRGIFTSEIGTKQITQSALLAEARSDYSEAAKQYDEALNKQDWVDGEPTE
AEKDFWELASLDCYNHLAEWKSLEYCSTASIDSEKIWSEPFYQETYLPYM
IRSKLKLLLQGEADQSLLTFIDKAMHGELQKAILELHYSQELSLLYLLQD
DVDRAKYYIQNGIQSFMQNYSSIDVLLHQSRLTKLQSVQALTEIQEFISF
ISKQGNLSSQVPLKRLLNTWTNRYPDAKMDPMNIWDDIITNRCFFLSKIE
EKLDISSLIRSCKFSMKMKMIDSARKQNNFSLAMKLLKELHKESKTRDDW
LVSWVQSYCRLSHCRSRSQGCSEQVLTVLKTVSLLDENNVSSYLSKNILA
FRDQNILLGTTYRIIANALSSEPACLAEIEEDKARRILELSGEDSEKVIA
GLYQRAFQHLSEAVQAAEEEAGVIDAYMTLADFCDQQLRKEEEAYPALVV
EKMLKALKLNSNEARLKFPRLLQIIERYPEETLSLMTKEISSVPCWQFIS
WISHMVALLDKDQAVAVQHSVEEITDNYPQAIVYPFIISSESTSTGHKNK
EFVARIKSKLDQGGVIQDFINALDQLSNPELLFKDWSNDVRAELAVNKKN
IEKMYERMYAALGDPKAPGLGAFRRKFIQTFGKEFDKHFGKGSDFNDITN
MLLLKMNKDSKPPGNLKECSPWMSDFKVEFLRNELEIPGQYDGRGKPLPE
YHVRIAGFDERVTVMASLRRPKRIIIRGHDEREHPFLVKGGEDLRQDQRV
EQLFQVMNGILAQDSACSQRALQLRTYSVVPMTSRLGLIEWLENTVTLKD
LLLNTMSQEEKAAYLSDPRAPPCEYKDWLDVGAYMLMYKGANRTETVTSF
RKRESKVPADLLKRAFVRMSTSPEAFLALRSHFASSHALICISHWILGIG
DRHLNNFMVAMETGGVIGIDFGHAFGSATQFLPVPELMPFRLTRQFINLM
LPMKETGLMYSIMVHALRAFRSDPGLLTNTMDVFVKEPSFDWKNWYPRQK
ICYAKRKLAGANPAVITCDELLLGHEKAPAFRDYVAVARGSKDHNIRAQE
PESGLSEETQVKCLMDQATDPNILGRTWEGWEPWM

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

K263 R264 N305 R2228 K2738 M2742 R2745

K249 R250 N291 R1875 K2264 M2268 R2271

BS02

dna

D168 T169 V170 P218 K452 M2742 Y2743 R2745 K2746

D159 T160 V161 P209 K427 M2268 Y2269 R2271 K2272

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

protein binding

ATP binding

kinase activity

enzyme binding

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

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

DNA damage response

brain development

heart development

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

Cellular Component

GO:0000781

chromosome, telomeric region

chromatin

nucleus

nucleoplasm

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

PDB	RCSB:8bot, PDBe:8bot, PDBj:8bot
PDBsum	8bot
PubMed	37311458
UniProt	P78527\|PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit (Gene Name=PRKDC)

Structure of PDB 8bot Chain F