9QMS | pdb_00009qms

DNA-PK bound to 153 bp H2AX nucleosome with ATPyS

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
I [auth E]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
M [auth a]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
S [auth e]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
E [auth A]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
V [auth M]SCOP2B SuperfamilyvWA-like 8035574 3000832 SCOP2B (2022-06-29)
V [auth M]SCOP2B SuperfamilySPOC domain-like 8035571 3000675 SCOP2B (2022-06-29)
U [auth K]SCOP2B SuperfamilySPOC domain-like 8035571 3000675 SCOP2B (2022-06-29)
U [auth K]SCOP2B SuperfamilyvWA-like 8035574 3000832 SCOP2B (2022-06-29)
DA [auth m]SCOP2B SuperfamilySPOC domain-like 8035571 3000675 SCOP2B (2022-06-29)
DA [auth m]SCOP2B SuperfamilyvWA-like 8035574 3000832 SCOP2B (2022-06-29)
BA [auth k]SCOP2B SuperfamilyvWA-like 8035574 3000832 SCOP2B (2022-06-29)
BA [auth k]SCOP2B SuperfamilySPOC domain-like 8035571 3000675 SCOP2B (2022-06-29)
J [auth F]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
N [auth b]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
T [auth f]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
F [auth B]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
B [auth L]SCOP2B SuperfamilyC-terminal domain of Ku80 8041016 3001210 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)
CA [auth n]SCOP2B SuperfamilyvWA-like 8035579 3000832 SCOP2B (2022-06-29)
CA [auth n]SCOP2B SuperfamilySPOC domain-like 8035577 3000675 SCOP2B (2022-06-29)
P [auth N]SCOP2B SuperfamilyvWA-like 8035579 3000832 SCOP2B (2022-06-29)
P [auth N]SCOP2B SuperfamilySPOC domain-like 8035577 3000675 SCOP2B (2022-06-29)
AA [auth l]SCOP2B SuperfamilySPOC domain-like 8035577 3000675 SCOP2B (2022-06-29)
AA [auth l]SCOP2B SuperfamilyvWA-like 8035579 3000832 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
E [auth A],
I [auth E],
M [auth a],
S [auth e]		PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
BA [auth k],
DA [auth m],
U [auth K],
V [auth M]		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
BA [auth k],
DA [auth m],
U [auth K],
V [auth M]		PF03730Ku70/Ku80 C-terminal arm (Ku_C)Ku70/Ku80 C-terminal arm- Family
BA [auth k],
DA [auth m],
U [auth K],
V [auth M]		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
F [auth B],
J [auth F],
N [auth b],
T [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
C,
G,
K [auth c],
Q [auth g]		PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
AA [auth l],
B [auth L],
CA [auth n],
P [auth N]		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
AA [auth l],
B [auth L],
CA [auth n],
P [auth N]		PF08785Ku C terminal domain like (Ku_PK_bind)Ku C terminal domain likeThe non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA ...The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C terminal of Ku which binds to DNA-PKcs [1].
Domain
AA [auth l],
B [auth L],
CA [auth n],
P [auth N]		PF03730Ku70/Ku80 C-terminal arm (Ku_C)Ku70/Ku80 C-terminal arm- Family
AA [auth l],
B [auth L],
CA [auth n],
P [auth N]		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 O],
O [auth o]		PF08163DNA-dependent protein kinase catalytic subunit, CC3 (DNAPKcs_CC3)DNA-dependent protein kinase catalytic subunit, CC3- Repeat
A [auth O],
O [auth o]		PF02260FATC domain (FATC)FATC domain- Family
A [auth O],
O [auth o]		PF00454Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)Phosphatidylinositol 3- and 4-kinase- Family
A [auth O],
O [auth o]		PF19704DNA-PKcs, CC5 (DNAPKcs_CC5)DNA-PKcs, CC5- Repeat
A [auth O],
O [auth o]		PF20502DNA-dependent protein kinase catalytic subunit, CC1/2 (DNAPKcs_CC1-2)DNA-dependent protein kinase catalytic subunit, CC1/2- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
E [auth A],
I [auth E],
M [auth a],
S [auth e]		Histone H3.1
X [auth J],
Z [auth j]		DNA---
W [auth I],
Y [auth i]		DNA---
BA [auth k],
DA [auth m],
U [auth K],
V [auth M]		X-ray repair cross-complementing protein 6
F [auth B],
J [auth F],
N [auth b],
T [auth f]		Histone H4
D,
H,
L [auth d],
R [auth h]		Histone H2B type 1-J
C,
G,
K [auth c],
Q [auth g]		Histone H2AX
AA [auth l],
B [auth L],
CA [auth n],
P [auth N]		X-ray repair cross-complementing protein 5
A [auth O],
O [auth o]		DNA-dependent protein kinase catalytic subunit

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
E [auth A],
I [auth E],
M [auth a],
S [auth e]		Pharos:  P68431
BA [auth k],
DA [auth m],
U [auth K],
V [auth M]		Pharos:  P12956
F [auth B],
J [auth F],
N [auth b],
T [auth f]		Pharos:  P62805
D,
H,
L [auth d],
R [auth h]		Pharos:  P06899
C,
G,
K [auth c],
Q [auth g]		Pharos:  P16104
AA [auth l],
B [auth L],
CA [auth n],
P [auth N]		Pharos:  P13010
A [auth O],
O [auth o]		Pharos:  P78527