General information
PDB ID 6ERF
Title COMPLEX OF APLF FACTOR AND KU HETERODIMER BOUND TO DNA
PDB header DNA BINDING PROTEIN
Date 2017-10-18
Experimental method X-RAY DIFFRACTION
Resolution (A) 3.01
Kind dna
Organism HOMO SAPIENS, SYNTHETIC CONSTRUCT
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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:
pdb6erf.pdb ABCDEFGHQRST IJKLMNOP 0
Biounits:
6erf.pdb1.pdb ABQ IJ 1
6erf.pdb2.pdb CDR KL 1
6erf.pdb3.pdb EFS MN 1
6erf.pdb4.pdb GHT OP 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 5.1e-75 1 CL0128 A 37 256   
Ku Domain P12956_263-468 3e-49 1 CL0616 A 263 468 IJ  L-Bb L-Mj 
Ku_N Domain P13010_9-244 9.4e-59 1 CL0128 B 9 244   
Ku Domain P13010_253-453 9.9e-44 1 CL0616 B 253 453 IJ  S-Bb L-Bb 
Ku_N Domain P12956_37-256 4e-76 1 CL0128 C 37 256   
Ku Domain P12956_263-468 1.1e-50 1 CL0616 C 263 468 KL  L-Bb L-Mj 
Ku_N Domain P13010_9-244 1.5e-57 1 CL0128 D 9 244   
Ku Domain P13010_253-453 9.8e-44 1 CL0616 D 253 453 KL  S-Bb L-Bb 
Ku_N Domain P12956_37-256 7.1e-76 1 CL0128 E 37 256   
Ku Domain P12956_263-468 1.4e-50 1 CL0616 E 263 468 MN  L-Bb L-Mj 
Ku_N Domain P13010_9-244 8.8e-63 1 CL0128 F 9 244   
Ku Domain P13010_253-453 1e-43 1 CL0616 F 253 453 MN  S-Bb L-Bb 
Ku_N Domain P12956_37-256 5.2e-75 1 CL0128 G 37 256 O  L-Bb 
Ku Domain P12956_263-468 1.1e-50 1 CL0616 G 263 468 OP  L-Bb L-Mj 
Ku_N Domain P13010_9-244 8.8e-63 1 CL0128 H 9 244   
Ku Domain P13010_253-453 1e-43 1 CL0616 H 253 453 OP  S-Bb L-Bb 
Ku_C Family P12956_472-534 3.5e-23 1 No_clan A 472 535   
Ku_C Family P13010_476-545 2.9e-11 1 No_clan B 476 542   
Ku_C Family P12956_472-534 1.6e-23 1 No_clan C 472 538   
Ku_C Family P13010_476-545 2.9e-11 1 No_clan D 476 542   
Ku_C Family P12956_472-534 3.6e-23 1 No_clan E 472 535   
Ku_C Family P13010_476-545 3e-11 1 No_clan F 476 542   
Ku_C Family P12956_472-534 9.1e-23 1 No_clan G 472 534   
Ku_C Family P13010_476-545 3e-11 1 No_clan H 476 542   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/C/E/G=1-544 C cytosol
A/C/E/G=1-544 C extracellular region
A/C/E/G=1-544 C ficolin-1-rich granule lumen
A/C/E/G=1-544 C Ku70:Ku80 complex
A/C/E/G=1-544 C membrane
A/C/E/G=1-544 C nonhomologous end joining complex
A/C/E/G=1-544 C nuclear chromosome, telomeric region
A/C/E/G=1-544 C nuclear telomere cap complex
A/C/E/G=1-544 C nucleolus
A/C/E/G=1-544 C nucleoplasm
A/C/E/G=1-544 C nucleus
A/C/E/G=1-544 C protein-containing complex
A/C/E/G=1-544 C protein-DNA complex
A/C/E/G=1-544 C secretory granule lumen
A/C/E/G=1-544 C transcription regulator complex
A/C/E/G=1-544 F 5'-deoxyribose-5-phosphate lyase activity
A/C/E/G=1-544 F ATP binding
A/C/E/G=1-544 F cyclin binding
A/C/E/G=1-544 F damaged DNA binding
A/C/E/G=1-544 F DNA binding
A/C/E/G=1-544 F DNA helicase activity
A/C/E/G=1-544 F double-stranded DNA binding
A/C/E/G=1-544 F protein C-terminus binding
A/C/E/G=1-544 F protein-containing complex binding
A/C/E/G=1-544 F RNA binding
A/C/E/G=1-544 F telomeric DNA binding
A/C/E/G=1-544 F transcription regulatory region sequence-specific DNA binding
A/C/E/G=1-544 P activation of innate immune response
A/C/E/G=1-544 P brain development
A/C/E/G=1-544 P cellular hyperosmotic salinity response
A/C/E/G=1-544 P cellular response to gamma radiation
A/C/E/G=1-544 P cellular response to X-ray
A/C/E/G=1-544 P DNA ligation
A/C/E/G=1-544 P DNA recombination
A/C/E/G=1-544 P double-strand break repair via classical nonhomologous end joining
A/C/E/G=1-544 P double-strand break repair via nonhomologous end joining
A/C/E/G=1-544 P establishment of integrated proviral latency
A/C/E/G=1-544 P innate immune response
A/C/E/G=1-544 P negative regulation of transcription, DNA-templated
A/C/E/G=1-544 P neutrophil degranulation
A/C/E/G=1-544 P positive regulation of lymphocyte differentiation
A/C/E/G=1-544 P positive regulation of protein kinase activity
A/C/E/G=1-544 P positive regulation of transcription by RNA polymerase II
A/C/E/G=1-544 P positive regulation of transcription, DNA-templated
A/C/E/G=1-544 P positive regulation of type I interferon production
A/C/E/G=1-544 P regulation of smooth muscle cell proliferation
A/C/E/G=1-544 P telomere maintenance
B/D/F/H=2-555 C cytosol
B/D/F/H=2-555 C extracellular region
B/D/F/H=2-555 C Ku70:Ku80 complex
B/D/F/H=2-555 C membrane
B/D/F/H=2-555 C nonhomologous end joining complex
B/D/F/H=2-555 C nuclear chromosome, telomeric region
B/D/F/H=2-555 C nuclear telomere cap complex
B/D/F/H=2-555 C nucleolus
B/D/F/H=2-555 C nucleoplasm
B/D/F/H=2-555 C nucleus
B/D/F/H=2-555 C plasma membrane
B/D/F/H=2-555 C protein-containing complex
B/D/F/H=2-555 C protein-DNA complex
B/D/F/H=2-555 C ribonucleoprotein complex
B/D/F/H=2-555 C secretory granule lumen
B/D/F/H=2-555 C site of DNA damage
B/D/F/H=2-555 C small-subunit processome
B/D/F/H=2-555 F ATP binding
B/D/F/H=2-555 F damaged DNA binding
B/D/F/H=2-555 F DNA binding
B/D/F/H=2-555 F DNA end binding
B/D/F/H=2-555 F DNA helicase activity
B/D/F/H=2-555 F double-stranded DNA binding
B/D/F/H=2-555 F enzyme activator activity
B/D/F/H=2-555 F protein C-terminus binding
B/D/F/H=2-555 F protein-containing complex binding
B/D/F/H=2-555 F RNA binding
B/D/F/H=2-555 F telomeric DNA binding
B/D/F/H=2-555 F transcription regulatory region sequence-specific DNA binding
B/D/F/H=2-555 F U3 snoRNA binding
B/D/F/H=2-555 F ubiquitin protein ligase binding
B/D/F/H=2-555 P activation of innate immune response
B/D/F/H=2-555 P brain development
B/D/F/H=2-555 P cell population proliferation
B/D/F/H=2-555 P cellular hyperosmotic salinity response
B/D/F/H=2-555 P cellular response to DNA damage stimulus
B/D/F/H=2-555 P cellular response to fatty acid
B/D/F/H=2-555 P cellular response to gamma radiation
B/D/F/H=2-555 P cellular response to leukemia inhibitory factor
B/D/F/H=2-555 P cellular response to X-ray
B/D/F/H=2-555 P DNA recombination
B/D/F/H=2-555 P double-strand break repair
B/D/F/H=2-555 P double-strand break repair via nonhomologous end joining
B/D/F/H=2-555 P establishment of integrated proviral latency
B/D/F/H=2-555 P hematopoietic stem cell differentiation
B/D/F/H=2-555 P innate immune response
B/D/F/H=2-555 P negative regulation of t-circle formation
B/D/F/H=2-555 P negative regulation of transcription, DNA-templated
B/D/F/H=2-555 P neutrophil degranulation
B/D/F/H=2-555 P positive regulation of catalytic activity
B/D/F/H=2-555 P positive regulation of neurogenesis
B/D/F/H=2-555 P positive regulation of protein kinase activity
B/D/F/H=2-555 P positive regulation of telomerase activity
B/D/F/H=2-555 P positive regulation of telomere maintenance via telomerase
B/D/F/H=2-555 P positive regulation of type I interferon production
B/D/F/H=2-555 P protein localization to chromosome, telomeric region
B/D/F/H=2-555 P regulation of smooth muscle cell proliferation
B/D/F/H=2-555 P regulation of telomere maintenance
B/D/F/H=2-555 P response to drug
B/D/F/H=2-555 P small-subunit processome assembly
B/D/F/H=2-555 P telomere maintenance
Q/R/S/T=174-191 C cytosol
Q/R/S/T=174-191 C nucleoplasm
Q/R/S/T=174-191 C nucleus
Q/R/S/T=174-191 C site of double-strand break
Q/R/S/T=174-191 F 3'-5' exonuclease activity
Q/R/S/T=174-191 F DNA-(apurinic or apyrimidinic site) endonuclease activity
Q/R/S/T=174-191 F endodeoxyribonuclease activity
Q/R/S/T=174-191 F metal ion binding
Q/R/S/T=174-191 F nucleotide binding
Q/R/S/T=174-191 P cellular response to DNA damage stimulus
Q/R/S/T=174-191 P double-strand break repair
Q/R/S/T=174-191 P positive regulation of DNA ligation
Q/R/S/T=174-191 P regulation of isotype switching
Q/R/S/T=174-191 P single strand break repair
Sequences
Download file with secondary structure created by Stride  
6erf.pdb1.pdb:   [ download sequences in FASTA format ]
I (dna): 
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J (dna): 
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A (protein): 
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B (protein): 
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Q (protein): 
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6erf.pdb2.pdb:   [ download sequences in FASTA format ]
K (dna): 
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L (dna): 
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C (protein): 
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D (protein): 
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R (protein): 
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6erf.pdb3.pdb:   [ download sequences in FASTA format ]
M (dna): 
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N (dna): 
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E (protein): 
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F (protein): 
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S (protein): 
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6erf.pdb4.pdb:   [ download sequences in FASTA format ]
O (dna): 
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P (dna): 
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G (protein): 
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H (protein): 
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T (protein): 
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