General information
PDB ID 5Y3R
Title CRYO-EM STRUCTURE OF HUMAN DNA-PK HOLOENZYME
PDB header DNA BINDING PROTEIN
Date 2017-07-29
Experimental method ELECTRON MICROSCOPY
Resolution (A) 6.6
Kind dna
Organism HOMO SAPIENS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb5y3r.pdb ABKC DE 0
Biounits:
5y3r.pdb1.pdb ABKC DE 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Ku_N Domain P12956_37-256 7.9e-73 1 CL0128 A 37 256 DE  L-Bb 
Ku Domain P12956_263-468 1.1e-50 1 CL0616 A 263 468 DE  H-Bb L-Bb L-Mn 
Ku_N Domain P13010_9-244 9.2e-62 1 CL0128 B 9 244   
Ku Domain P13010_253-453 1e-43 1 CL0616 B 253 453 DE  S-Bb L-Bb L-Mn 
NUC194 Domain P78527_1816-2202 3.9e-147 1 No_clan C 1754 2202   
Ku_C Family P12956_472-534 9.1e-23 1 No_clan A 472 534   
Ku_C Family P13010_476-545 3.6e-11 1 No_clan B 476 541 D  H-Bb 
DNAPKcs_CC5 Family P78527_1968-2332 5.4e-185 1 No_clan C 2213 2774   
PI3_PI4_kinase Family P78527_3747-4015 3.8e-65 1 CL0016 C 3747 4015   
DNAPKcs_CC5 Family P78527_2330-2456 2.6e-50 1 No_clan C 2575 2898   
FATC Family P78527_4097-4128 1.6e-08 1 No_clan C 4097 4128   
FAT Repeat P78527_3023-3470 2.9e-76 1 CL0020 C 3023 3470   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A=34-534 C cytosol
A=34-534 C extracellular region
A=34-534 C ficolin-1-rich granule lumen
A=34-534 C Ku70:Ku80 complex
A=34-534 C membrane
A=34-534 C nonhomologous end joining complex
A=34-534 C nuclear chromosome, telomeric region
A=34-534 C nuclear telomere cap complex
A=34-534 C nucleolus
A=34-534 C nucleoplasm
A=34-534 C nucleus
A=34-534 C protein-containing complex
A=34-534 C protein-DNA complex
A=34-534 C secretory granule lumen
A=34-534 C transcription regulator complex
A=34-534 F 5'-deoxyribose-5-phosphate lyase activity
A=34-534 F ATP binding
A=34-534 F cyclin binding
A=34-534 F damaged DNA binding
A=34-534 F DNA binding
A=34-534 F DNA helicase activity
A=34-534 F double-stranded DNA binding
A=34-534 F protein C-terminus binding
A=34-534 F protein-containing complex binding
A=34-534 F RNA binding
A=34-534 F telomeric DNA binding
A=34-534 F transcription regulatory region sequence-specific DNA binding
A=34-534 P activation of innate immune response
A=34-534 P brain development
A=34-534 P cellular hyperosmotic salinity response
A=34-534 P cellular response to gamma radiation
A=34-534 P cellular response to X-ray
A=34-534 P DNA ligation
A=34-534 P DNA recombination
A=34-534 P double-strand break repair via classical nonhomologous end joining
A=34-534 P double-strand break repair via nonhomologous end joining
A=34-534 P establishment of integrated proviral latency
A=34-534 P innate immune response
A=34-534 P negative regulation of transcription, DNA-templated
A=34-534 P neutrophil degranulation
A=34-534 P positive regulation of lymphocyte differentiation
A=34-534 P positive regulation of protein kinase activity
A=34-534 P positive regulation of transcription by RNA polymerase II
A=34-534 P positive regulation of transcription, DNA-templated
A=34-534 P positive regulation of type I interferon production
A=34-534 P regulation of smooth muscle cell proliferation
A=34-534 P telomere maintenance
B=6-541 C cytosol
B=6-541 C extracellular region
B=6-541 C Ku70:Ku80 complex
B=6-541 C membrane
B=6-541 C nonhomologous end joining complex
B=6-541 C nuclear chromosome, telomeric region
B=6-541 C nuclear telomere cap complex
B=6-541 C nucleolus
B=6-541 C nucleoplasm
B=6-541 C nucleus
B=6-541 C plasma membrane
B=6-541 C protein-containing complex
B=6-541 C protein-DNA complex
B=6-541 C ribonucleoprotein complex
B=6-541 C secretory granule lumen
B=6-541 C site of DNA damage
B=6-541 C small-subunit processome
B=6-541 F ATP binding
B=6-541 F damaged DNA binding
B=6-541 F DNA binding
B=6-541 F DNA end binding
B=6-541 F DNA helicase activity
B=6-541 F double-stranded DNA binding
B=6-541 F enzyme activator activity
B=6-541 F protein C-terminus binding
B=6-541 F protein-containing complex binding
B=6-541 F RNA binding
B=6-541 F telomeric DNA binding
B=6-541 F transcription regulatory region sequence-specific DNA binding
B=6-541 F U3 snoRNA binding
B=6-541 F ubiquitin protein ligase binding
B=6-541 P activation of innate immune response
B=6-541 P brain development
B=6-541 P cell population proliferation
B=6-541 P cellular hyperosmotic salinity response
B=6-541 P cellular response to DNA damage stimulus
B=6-541 P cellular response to fatty acid
B=6-541 P cellular response to gamma radiation
B=6-541 P cellular response to leukemia inhibitory factor
B=6-541 P cellular response to X-ray
B=6-541 P DNA recombination
B=6-541 P double-strand break repair
B=6-541 P double-strand break repair via nonhomologous end joining
B=6-541 P establishment of integrated proviral latency
B=6-541 P hematopoietic stem cell differentiation
B=6-541 P innate immune response
B=6-541 P negative regulation of t-circle formation
B=6-541 P negative regulation of transcription, DNA-templated
B=6-541 P neutrophil degranulation
B=6-541 P positive regulation of catalytic activity
B=6-541 P positive regulation of neurogenesis
B=6-541 P positive regulation of protein kinase activity
B=6-541 P positive regulation of telomerase activity
B=6-541 P positive regulation of telomere maintenance via telomerase
B=6-541 P positive regulation of type I interferon production
B=6-541 P protein localization to chromosome, telomeric region
B=6-541 P regulation of smooth muscle cell proliferation
B=6-541 P regulation of telomere maintenance
B=6-541 P response to drug
B=6-541 P small-subunit processome assembly
B=6-541 P telomere maintenance
C=10-4128 C cytosol
C=10-4128 C DNA-dependent protein kinase-DNA ligase 4 complex
C=10-4128 C membrane
C=10-4128 C nonhomologous end joining complex
C=10-4128 C nuclear chromosome, telomeric region
C=10-4128 C nucleolus
C=10-4128 C nucleoplasm
C=10-4128 C nucleus
C=10-4128 C protein-containing complex
C=10-4128 C protein-DNA complex
C=10-4128 C small-subunit processome
C=10-4128 C transcription regulator complex
C=10-4128 F ATP binding
C=10-4128 F DNA-dependent protein kinase activity
C=10-4128 F double-stranded DNA binding
C=10-4128 F enzyme binding
C=10-4128 F protein domain specific binding
C=10-4128 F protein kinase activity
C=10-4128 F protein serine/threonine kinase activity
C=10-4128 F RNA binding
C=10-4128 F transcription factor binding
C=10-4128 F U3 snoRNA binding
C=10-4128 P activation of innate immune response
C=10-4128 P B cell lineage commitment
C=10-4128 P brain development
C=10-4128 P cellular protein modification process
C=10-4128 P cellular response to DNA damage stimulus
C=10-4128 P cellular response to insulin stimulus
C=10-4128 P double-strand break repair
C=10-4128 P double-strand break repair via alternative nonhomologous end joining
C=10-4128 P double-strand break repair via nonhomologous end joining
C=10-4128 P ectopic germ cell programmed cell death
C=10-4128 P heart development
C=10-4128 P immunoglobulin V(D)J recombination
C=10-4128 P innate immune response
C=10-4128 P intrinsic apoptotic signaling pathway in response to DNA damage
C=10-4128 P maturation of 5.8S rRNA
C=10-4128 P negative regulation of apoptotic process
C=10-4128 P negative regulation of cellular senescence
C=10-4128 P negative regulation of immunoglobulin production
C=10-4128 P negative regulation of protein phosphorylation
C=10-4128 P negative regulation of response to gamma radiation
C=10-4128 P peptidyl-serine phosphorylation
C=10-4128 P peptidyl-threonine phosphorylation
C=10-4128 P positive regulation of apoptotic process
C=10-4128 P positive regulation of developmental growth
C=10-4128 P positive regulation of double-strand break repair via nonhomologous end joining
C=10-4128 P positive regulation of erythrocyte differentiation
C=10-4128 P positive regulation of fibroblast proliferation
C=10-4128 P positive regulation of lymphocyte differentiation
C=10-4128 P positive regulation of platelet formation
C=10-4128 P positive regulation of transcription by RNA polymerase II
C=10-4128 P positive regulation of translation
C=10-4128 P positive regulation of type I interferon production
C=10-4128 P pro-B cell differentiation
C=10-4128 P protein destabilization
C=10-4128 P protein phosphorylation
C=10-4128 P protein ubiquitination
C=10-4128 P regulation of circadian rhythm
C=10-4128 P regulation of epithelial cell proliferation
C=10-4128 P regulation of hematopoietic stem cell differentiation
C=10-4128 P regulation of smooth muscle cell proliferation
C=10-4128 P response to activity
C=10-4128 P response to gamma radiation
C=10-4128 P rhythmic process
C=10-4128 P signal transduction involved in mitotic G1 DNA damage checkpoint
C=10-4128 P small-subunit processome assembly
C=10-4128 P somitogenesis
C=10-4128 P spleen development
C=10-4128 P T cell differentiation in thymus
C=10-4128 P T cell lineage commitment
C=10-4128 P T cell receptor V(D)J recombination
C=10-4128 P telomere capping
C=10-4128 P telomere maintenance
C=10-4128 P thymus development
Sequences
Download file with secondary structure created by Stride  
5y3r.pdb1.pdb:   [ download sequences in FASTA format ]
D (dna): 
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E (dna): 
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A (protein): 
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B (protein): 
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C (protein): 
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K (protein): 
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