9QCR | pdb_00009qcr

DNA-PK bound to 153 bp H2AX nucleosome model 2


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
K [auth F]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
G [auth B]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
J [auth E]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
F [auth A]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
B [auth L]SCOP2B SuperfamilyvWA-like 8035579 3000832 SCOP2B (2022-06-29)
B [auth L]SCOP2B SuperfamilySPOC domain-like 8035577 3000675 SCOP2B (2022-06-29)
A [auth K]SCOP2B SuperfamilySPOC domain-like 8035571 3000675 SCOP2B (2022-06-29)
A [auth K]SCOP2B SuperfamilyvWA-like 8035574 3000832 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
G [auth B],
K [auth F]
PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].
Domain
F [auth A],
J [auth E]
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
D [auth C],
H [auth G]
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
C [auth O]PF08163DNA-dependent protein kinase catalytic subunit, CC3 (DNAPKcs_CC3)DNA-dependent protein kinase catalytic subunit, CC3- Repeat
C [auth O]PF02260FATC domain (FATC)FATC domain- Family
C [auth O]PF00454Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)Phosphatidylinositol 3- and 4-kinase- Family
C [auth O]PF19704DNA-PKcs, CC5 (DNAPKcs_CC5)DNA-PKcs, CC5- Repeat
C [auth O]PF20502DNA-dependent protein kinase catalytic subunit, CC1/2 (DNAPKcs_CC1-2)DNA-dependent protein kinase catalytic subunit, CC1/2- Repeat
B [auth L]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
B [auth L]PF03730Ku70/Ku80 C-terminal arm (Ku_C)Ku70/Ku80 C-terminal arm- Family
B [auth L]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
A [auth K]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
A [auth K]PF03730Ku70/Ku80 C-terminal arm (Ku_C)Ku70/Ku80 C-terminal arm- Family
A [auth K]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
M [auth J]153 bp DNA---
L [auth I]153 bp DNA---
G [auth B],
K [auth F]
Histone H4
F [auth A],
J [auth E]
Histone H3.1
E [auth D],
I [auth H]
Histone H2B type 1-J
D [auth C],
H [auth G]
Histone H2AX
C [auth O]DNA-dependent protein kinase catalytic subunit
B [auth L]X-ray repair cross-complementing protein 5
A [auth K]X-ray repair cross-complementing protein 6

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
G [auth B],
K [auth F]
IPR009072Histone-foldHomologous Superfamily
G [auth B],
K [auth F]
IPR035425CENP-T/Histone H4, histone foldDomain
G [auth B],
K [auth F]
IPR001951Histone H4Family
G [auth B],
K [auth F]
IPR019809Histone H4, conserved siteConserved Site
G [auth B],
K [auth F]
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
F [auth A],
J [auth E]
IPR009072Histone-foldHomologous Superfamily
F [auth A],
J [auth E]
IPR007125Core Histone H2A/H2B/H3 domainDomain
F [auth A],
J [auth E]
IPR000164Histone H3/CENP-AFamily
E [auth D],
I [auth H]
IPR009072Histone-foldHomologous Superfamily
E [auth D],
I [auth H]
IPR000558Histone H2BFamily
E [auth D],
I [auth H]
IPR007125Core Histone H2A/H2B/H3 domainDomain
E [auth D],
I [auth H]
IPR055333Histone H2B, conserved siteConserved Site
D [auth C],
H [auth G]
IPR002119Histone H2AFamily
D [auth C],
H [auth G]
IPR007125Core Histone H2A/H2B/H3 domainDomain
D [auth C],
H [auth G]
IPR032454Histone H2A, C-terminal domainDomain
D [auth C],
H [auth G]
IPR032458Histone H2A conserved siteConserved Site
D [auth C],
H [auth G]
IPR009072Histone-foldHomologous Superfamily
C [auth O]IPR016024Armadillo-type foldHomologous Superfamily
C [auth O]IPR003151PIK-related kinase, FATDomain
C [auth O]IPR046803DNA-dependent protein kinase catalytic subunit, CC1/2Domain
C [auth O]IPR046804DNA-PKcs, N-terminalDomain
C [auth O]IPR045581DNA-dependent protein kinase catalytic subunit, CC5Domain
C [auth O]IPR003152FATC domainDomain
C [auth O]IPR012582DNA-dependent protein kinase catalytic subunit, CC3Domain
C [auth O]IPR011989Armadillo-like helicalHomologous Superfamily
C [auth O]IPR000403Phosphatidylinositol 3-/4-kinase, catalytic domainDomain
C [auth O]IPR050517DNA Damage Response and Repair KinaseFamily
C [auth O]IPR018936Phosphatidylinositol 3-/4-kinase, conserved siteConserved Site
C [auth O]IPR036940Phosphatidylinositol 3-/4-kinase, catalytic domain superfamilyHomologous Superfamily
C [auth O]IPR011009Protein kinase-like domain superfamilyHomologous Superfamily
C [auth O]IPR037706DNA-dependent protein kinase catalytic subunit, catalytic domainDomain
C [auth O]IPR014009PIK-related kinase, FAT domainDomain
B [auth L]IPR036494Ku, C-terminal domain superfamilyHomologous Superfamily
B [auth L]IPR016194SPOC-like, C-terminal domain superfamilyHomologous Superfamily
B [auth L]IPR036465von Willebrand factor A-like domain superfamilyHomologous Superfamily
B [auth L]IPR002035von Willebrand factor, type ADomain
B [auth L]IPR005161Ku70/Ku80, N-terminal alpha/betaDomain
B [auth L]IPR014893Ku, C-terminalDomain
B [auth L]IPR006164Ku70/Ku80, DNA-binding domainDomain
B [auth L]IPR005160Ku70/Ku80 C-terminal armDomain
B [auth L]IPR024193Ku80Family
A [auth K]IPR016194SPOC-like, C-terminal domain superfamilyHomologous Superfamily
A [auth K]IPR027388Ku70, bridge and pillars domain superfamilyHomologous Superfamily
A [auth K]IPR036361SAP domain superfamilyHomologous Superfamily
A [auth K]IPR006165Ku70Family
A [auth K]IPR036465von Willebrand factor A-like domain superfamilyHomologous Superfamily
A [auth K]IPR005161Ku70/Ku80, N-terminal alpha/betaDomain
A [auth K]IPR006164Ku70/Ku80, DNA-binding domainDomain
A [auth K]IPR047087Ku70, core domainDomain
A [auth K]IPR005160Ku70/Ku80 C-terminal armDomain
A [auth K]IPR003034SAP domainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
G [auth B],
K [auth F]
PharosP62805
F [auth A],
J [auth E]
PharosP68431
E [auth D],
I [auth H]
PharosP06899
D [auth C],
H [auth G]
PharosP16104
C [auth O]PharosP78527
B [auth L]PharosP13010
A [auth K]PharosP12956