5Y3R | pdb_00005y3r

Cryo-EM structure of Human DNA-PK Holoenzyme

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2B SuperfamilySPOC domain-like 8035577 3000675 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyvWA-like 8035579 3000832 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyvWA-like 8035574 3000832 SCOP2B (2022-06-29)
ASCOP2B SuperfamilySPOC domain-like 8035571 3000675 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
F [auth C]e5y3rC1 A: Cryptochrome/photolyase FAD-binding domain-relatedX: Cryptochrome/photolyase FAD-binding domain-relatedH: PriXT: ChromoF:ECOD (20:10:01)
Be5y3rB1 A: TIM beta/alpha-barrelX: TIM barrelsH: TIM barrelsT: FATCF:ECOD (20:10:01)
Ae5y3rA1 A: TIM beta/alpha-barrelX: TIM barrelsH: TIM barrelsT: FATCF:ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
F [auth C]PF08163DNA-dependent protein kinase catalytic subunit, CC3 (DNAPKcs_CC3)DNA-dependent protein kinase catalytic subunit, CC3- Repeat
F [auth C]PF02260FATC domain (FATC)FATC domain- Family
F [auth C]PF00454Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)Phosphatidylinositol 3- and 4-kinase- Family
F [auth C]PF19704DNA-PKcs, CC5 (DNAPKcs_CC5)DNA-PKcs, CC5- Repeat
F [auth C]PF02259FAT domain (FAT)FAT domain- Repeat
F [auth C]PF20502DNA-dependent protein kinase catalytic subunit, CC1/2 (DNAPKcs_CC1-2)DNA-dependent protein kinase catalytic subunit, CC1/2- Repeat
PF02735Ku70/Ku80 beta-barrel domain (Ku)Ku70/Ku80 beta-barrel domainThe Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-bi ...The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 Swiss:P12956 and Ku80 Swiss:P13010 proteins that form a DNA binding heterodimer [1].
Domain
PF03730Ku70/Ku80 C-terminal arm (Ku_C)Ku70/Ku80 C-terminal arm- Family
PF03731Ku70/Ku80 N-terminal alpha/beta domain (Ku_N)Ku70/Ku80 N-terminal alpha/beta domainThe Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal ...The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [1].
Domain
PF02735Ku70/Ku80 beta-barrel domain (Ku)Ku70/Ku80 beta-barrel domainThe Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-bi ...The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 Swiss:P12956 and Ku80 Swiss:P13010 proteins that form a DNA binding heterodimer [1].
Domain
PF03730Ku70/Ku80 C-terminal arm (Ku_C)Ku70/Ku80 C-terminal arm- Family
PF03731Ku70/Ku80 N-terminal alpha/beta domain (Ku_N)Ku70/Ku80 N-terminal alpha/beta domainThe Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal ...The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [1].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
F [auth C]DNA-dependent protein kinase catalytic subunit
DNA (36-MER)---
DNA (34-MER)---
C [auth K]PRKDC-Helix---
X-ray repair cross-complementing protein 5
X-ray repair cross-complementing protein 6

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
F [auth C]IPR016024Armadillo-type foldHomologous Superfamily
F [auth C]IPR003151PIK-related kinase, FATDomain
F [auth C]IPR046803DNA-dependent protein kinase catalytic subunit, CC1/2Domain
F [auth C]IPR046804DNA-PKcs, N-terminalDomain
F [auth C]IPR045581DNA-dependent protein kinase catalytic subunit, CC5Domain
F [auth C]IPR003152FATC domainDomain
F [auth C]IPR012582DNA-dependent protein kinase catalytic subunit, CC3Domain
F [auth C]IPR011989Armadillo-like helicalHomologous Superfamily
F [auth C]IPR000403Phosphatidylinositol 3-/4-kinase, catalytic domainDomain
F [auth C]IPR050517DNA Damage Response and Repair KinaseFamily
F [auth C]IPR018936Phosphatidylinositol 3-/4-kinase, conserved siteConserved Site
F [auth C]IPR036940Phosphatidylinositol 3-/4-kinase, catalytic domain superfamilyHomologous Superfamily
F [auth C]IPR011009Protein kinase-like domain superfamilyHomologous Superfamily
F [auth C]IPR037706DNA-dependent protein kinase catalytic subunit, catalytic domainDomain
F [auth C]IPR014009PIK-related kinase, FAT domainDomain
IPR036494Ku, C-terminal domain superfamilyHomologous Superfamily
IPR016194SPOC-like, C-terminal domain superfamilyHomologous Superfamily
IPR036465von Willebrand factor A-like domain superfamilyHomologous Superfamily
IPR002035von Willebrand factor, type ADomain
IPR005161Ku70/Ku80, N-terminal alpha/betaDomain
IPR014893Ku, C-terminalDomain
IPR006164Ku70/Ku80, DNA-binding domainDomain
IPR005160Ku70/Ku80 C-terminal armDomain
IPR024193Ku80Family
IPR016194SPOC-like, C-terminal domain superfamilyHomologous Superfamily
IPR027388Ku70, bridge and pillars domain superfamilyHomologous Superfamily
IPR036361SAP domain superfamilyHomologous Superfamily
IPR006165Ku70Family
IPR036465von Willebrand factor A-like domain superfamilyHomologous Superfamily
IPR005161Ku70/Ku80, N-terminal alpha/betaDomain
IPR006164Ku70/Ku80, DNA-binding domainDomain
IPR047087Ku70, core domainDomain
IPR005160Ku70/Ku80 C-terminal armDomain
IPR003034SAP domainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
F [auth C]Pharos:  P78527
Pharos:  P13010
Pharos:  P12956