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7K1N

CryoEM structure of inactivated-form DNA-PK (Complex V)

Functional Information from GO Data
ChainGOidnamespacecontents
A0000460biological_processmaturation of 5.8S rRNA
A0000723biological_processtelomere maintenance
A0000781cellular_componentchromosome, telomeric region
A0000785cellular_componentchromatin
A0001756biological_processsomitogenesis
A0001933biological_processnegative regulation of protein phosphorylation
A0002218biological_processactivation of innate immune response
A0002326biological_processB cell lineage commitment
A0002327biological_processimmature B cell differentiation
A0002328biological_processpro-B cell differentiation
A0002360biological_processT cell lineage commitment
A0003677molecular_functionDNA binding
A0003690molecular_functiondouble-stranded DNA binding
A0003723molecular_functionRNA binding
A0004672molecular_functionprotein kinase activity
A0004674molecular_functionprotein serine/threonine kinase activity
A0004677molecular_functionDNA-dependent protein kinase activity
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005667cellular_componenttranscription regulator complex
A0005730cellular_componentnucleolus
A0005829cellular_componentcytosol
A0005958cellular_componentDNA-dependent protein kinase-DNA ligase 4 complex
A0006281biological_processDNA repair
A0006302biological_processdouble-strand break repair
A0006303biological_processdouble-strand break repair via nonhomologous end joining
A0006310biological_processDNA recombination
A0006338biological_processchromatin remodeling
A0006468biological_processprotein phosphorylation
A0006974biological_processDNA damage response
A0007420biological_processbrain development
A0007507biological_processheart development
A0008630biological_processintrinsic apoptotic signaling pathway in response to DNA damage
A0010212biological_processresponse to ionizing radiation
A0010332biological_processresponse to gamma radiation
A0016020cellular_componentmembrane
A0016233biological_processtelomere capping
A0016301molecular_functionkinase activity
A0018105biological_processpeptidyl-serine phosphorylation
A0018107biological_processpeptidyl-threonine phosphorylation
A0019899molecular_functionenzyme binding
A0019904molecular_functionprotein domain specific binding
A0030098biological_processlymphocyte differentiation
A0031571biological_processmitotic G1 DNA damage checkpoint signaling
A0031648biological_processprotein destabilization
A0032040cellular_componentsmall-subunit processome
A0032869biological_processcellular response to insulin stimulus
A0032991cellular_componentprotein-containing complex
A0032993cellular_componentprotein-DNA complex
A0033077biological_processT cell differentiation in thymus
A0033151biological_processV(D)J recombination
A0033152biological_processimmunoglobulin V(D)J recombination
A0033153biological_processT cell receptor V(D)J recombination
A0034462biological_processsmall-subunit processome assembly
A0034511molecular_functionU3 snoRNA binding
A0035234biological_processectopic germ cell programmed cell death
A0035979molecular_functionhistone H2AXS139 kinase activity
A0036211biological_processprotein modification process
A0042254biological_processribosome biogenesis
A0042752biological_processregulation of circadian rhythm
A0043065biological_processpositive regulation of apoptotic process
A0043066biological_processnegative regulation of apoptotic process
A0045087biological_processinnate immune response
A0045621biological_processpositive regulation of lymphocyte differentiation
A0045648biological_processpositive regulation of erythrocyte differentiation
A0045727biological_processpositive regulation of translation
A0045944biological_processpositive regulation of transcription by RNA polymerase II
A0048511biological_processrhythmic process
A0048660biological_processregulation of smooth muscle cell proliferation
A0050678biological_processregulation of epithelial cell proliferation
A0051171biological_processobsolete regulation of nitrogen compound metabolic process
A0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
A0070418cellular_componentDNA-dependent protein kinase complex
A0070419cellular_componentnonhomologous end joining complex
A0080090biological_processregulation of primary metabolic process
A0080135biological_processregulation of cellular response to stress
A0097681biological_processdouble-strand break repair via alternative nonhomologous end joining
A0106310molecular_functionprotein serine kinase activity
A0160049biological_processnegative regulation of cGAS/STING signaling pathway
A1902036biological_processregulation of hematopoietic stem cell differentiation
A1905221biological_processpositive regulation of platelet formation
A2001034biological_processpositive regulation of double-strand break repair via nonhomologous end joining
B0000723biological_processtelomere maintenance
B0000725biological_processrecombinational repair
B0000781cellular_componentchromosome, telomeric region
B0000783cellular_componentnuclear telomere cap complex
B0000976molecular_functiontranscription cis-regulatory region binding
B0002218biological_processactivation of innate immune response
B0003677molecular_functionDNA binding
B0003678molecular_functionDNA helicase activity
B0003684molecular_functiondamaged DNA binding
B0003690molecular_functiondouble-stranded DNA binding
B0003691molecular_functiondouble-stranded telomeric DNA binding
B0003723molecular_functionRNA binding
B0004386molecular_functionhelicase activity
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005576cellular_componentextracellular region
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005667cellular_componenttranscription regulator complex
B0005694cellular_componentchromosome
B0005730cellular_componentnucleolus
B0005829cellular_componentcytosol
B0005958cellular_componentDNA-dependent protein kinase-DNA ligase 4 complex
B0006266biological_processDNA ligation
B0006281biological_processDNA repair
B0006303biological_processdouble-strand break repair via nonhomologous end joining
B0006310biological_processDNA recombination
B0008094molecular_functionATP-dependent activity, acting on DNA
B0010558biological_processnegative regulation of macromolecule biosynthetic process
B0016020cellular_componentmembrane
B0016787molecular_functionhydrolase activity
B0016829molecular_functionlyase activity
B0016887molecular_functionATP hydrolysis activity
B0030332molecular_functioncyclin binding
B0032508biological_processDNA duplex unwinding
B0032991cellular_componentprotein-containing complex
B0032993cellular_componentprotein-DNA complex
B0034774cellular_componentsecretory granule lumen
B0042162molecular_functiontelomeric DNA binding
B0043564cellular_componentKu70:Ku80 complex
B0044877molecular_functionprotein-containing complex binding
B0045027molecular_functionDNA end binding
B0045087biological_processinnate immune response
B0045621biological_processpositive regulation of lymphocyte differentiation
B0045860biological_processpositive regulation of protein kinase activity
B0045892biological_processnegative regulation of DNA-templated transcription
B0045893biological_processpositive regulation of DNA-templated transcription
B0045944biological_processpositive regulation of transcription by RNA polymerase II
B0048660biological_processregulation of smooth muscle cell proliferation
B0051575molecular_function5'-deoxyribose-5-phosphate lyase activity
B0070418cellular_componentDNA-dependent protein kinase complex
B0070419cellular_componentnonhomologous end joining complex
B0071475biological_processcellular hyperosmotic salinity response
B0071480biological_processcellular response to gamma radiation
B0071481biological_processcellular response to X-ray
B0097110molecular_functionscaffold protein binding
B0097680biological_processdouble-strand break repair via classical nonhomologous end joining
B1904813cellular_componentficolin-1-rich granule lumen
C0000723biological_processtelomere maintenance
C0000725biological_processrecombinational repair
C0000781cellular_componentchromosome, telomeric region
C0000783cellular_componentnuclear telomere cap complex
C0000976molecular_functiontranscription cis-regulatory region binding
C0002218biological_processactivation of innate immune response
C0003677molecular_functionDNA binding
C0003678molecular_functionDNA helicase activity
C0003684molecular_functiondamaged DNA binding
C0003690molecular_functiondouble-stranded DNA binding
C0003691molecular_functiondouble-stranded telomeric DNA binding
C0003723molecular_functionRNA binding
C0004386molecular_functionhelicase activity
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005576cellular_componentextracellular region
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005694cellular_componentchromosome
C0005730cellular_componentnucleolus
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0005886cellular_componentplasma membrane
C0005958cellular_componentDNA-dependent protein kinase-DNA ligase 4 complex
C0006281biological_processDNA repair
C0006302biological_processdouble-strand break repair
C0006303biological_processdouble-strand break repair via nonhomologous end joining
C0006310biological_processDNA recombination
C0006974biological_processDNA damage response
C0008047molecular_functionenzyme activator activity
C0008094molecular_functionATP-dependent activity, acting on DNA
C0009410biological_processresponse to xenobiotic stimulus
C0010558biological_processnegative regulation of macromolecule biosynthetic process
C0016020cellular_componentmembrane
C0016787molecular_functionhydrolase activity
C0016887molecular_functionATP hydrolysis activity
C0022008biological_processneurogenesis
C0031625molecular_functionubiquitin protein ligase binding
C0032040cellular_componentsmall-subunit processome
C0032204biological_processregulation of telomere maintenance
C0032212biological_processpositive regulation of telomere maintenance via telomerase
C0032508biological_processDNA duplex unwinding
C0032991cellular_componentprotein-containing complex
C0032993cellular_componentprotein-DNA complex
C0034462biological_processsmall-subunit processome assembly
C0034511molecular_functionU3 snoRNA binding
C0034774cellular_componentsecretory granule lumen
C0042162molecular_functiontelomeric DNA binding
C0042254biological_processribosome biogenesis
C0043085biological_processpositive regulation of catalytic activity
C0043564cellular_componentKu70:Ku80 complex
C0044877molecular_functionprotein-containing complex binding
C0045027molecular_functionDNA end binding
C0045087biological_processinnate immune response
C0045860biological_processpositive regulation of protein kinase activity
C0045892biological_processnegative regulation of DNA-templated transcription
C0048660biological_processregulation of smooth muscle cell proliferation
C0050769biological_processpositive regulation of neurogenesis
C0051575molecular_function5'-deoxyribose-5-phosphate lyase activity
C0051973biological_processpositive regulation of telomerase activity
C0060218biological_processhematopoietic stem cell differentiation
C0070198biological_processprotein localization to chromosome, telomeric region
C0070418cellular_componentDNA-dependent protein kinase complex
C0070419cellular_componentnonhomologous end joining complex
C0071398biological_processcellular response to fatty acid
C0071425biological_processhematopoietic stem cell proliferation
C0071475biological_processcellular hyperosmotic salinity response
C0071480biological_processcellular response to gamma radiation
C0071481biological_processcellular response to X-ray
C0090734cellular_componentsite of DNA damage
C1904430biological_processnegative regulation of t-circle formation
C1990830biological_processcellular response to leukemia inhibitory factor
C1990904cellular_componentribonucleoprotein complex
Functional Information from PROSITE/UniProt
site_idPS00915
Number of Residues15
DetailsPI3_4_KINASE_1 Phosphatidylinositol 3- and 4-kinases signature 1. VKgg.EDLRQDqrveQ
ChainResidueDetails
AVAL3752-GLN3766

site_idPS00916
Number of Residues21
DetailsPI3_4_KINASE_2 Phosphatidylinositol 3- and 4-kinases signature 2. ShAlicIshWILgIgDRHlnN
ChainResidueDetails
ASER3907-ASN3927

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues5
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
CLYS144
CLYS265
CLYS332
CLYS660
CLYS665

site_idSWS_FT_FI2
Number of Residues3
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163
ChainResidueDetails
CSER255
ALYS3642
CSER258
CSER318
BSER560
ALYS2259
ALYS3241
ALYS3260
ALYS3621
ALYS3638

site_idSWS_FT_FI3
Number of Residues1
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163
ChainResidueDetails
CTHR535
ASER687
ASER841
ASER1065
ASER2789
ASER3731
ASER3821

site_idSWS_FT_FI4
Number of Residues1
DetailsMOD_RES: Phosphoserine; by PRKDC => ECO:0000269|PubMed:10026262, ECO:0007744|PubMed:24275569
ChainResidueDetails
CSER577
BLYS331
BLYS338
BLYS461

site_idSWS_FT_FI5
Number of Residues1
DetailsMOD_RES: Phosphoserine; by PRKDC => ECO:0000305|PubMed:10026262
ChainResidueDetails
CSER579

site_idSWS_FT_FI6
Number of Residues1
DetailsMOD_RES: Phosphoserine; by PRKDC => ECO:0000269|PubMed:10026262
ChainResidueDetails
CSER580

site_idSWS_FT_FI7
Number of Residues1
DetailsMOD_RES: Phosphothreonine; by PRKDC => ECO:0000305|PubMed:10026262
ChainResidueDetails
CTHR715

site_idSWS_FT_FI8
Number of Residues7
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
ChainResidueDetails
CLYS195
CLYS532
CLYS534
CLYS566
CLYS669
CLYS688

site_idSWS_FT_FI9
Number of Residues1
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25114211, ECO:0007744|PubMed:28112733
ChainResidueDetails
CLYS568
ATHR2647

site_idSWS_FT_FI10
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
ChainResidueDetails
BLYS287
BLYS317

site_idSWS_FT_FI11
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:28112733
ChainResidueDetails
ASER4026
BLYS556

219140

PDB entries from 2024-05-01

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