AptaDB: Result

Interaction ID: 222

Aptamer sequence: AGCCGCGAGGGGAGGGAUAGGGUAGGGCGCGGCU

Target unique ID: P04626

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_218	SE15-8min	Protein	ERBB2_HUMAN	3.49 nM	20 mM HEPES (pH 7.0), 150 mM NaCl, 1 mM MgCl2, 2 mM DTT, and 40 U RNase Inhibitor	21749294

Aptamer Sequence:	AGCCGCGAGGGGAGGGAUAGGGUAGGGCGCGGCU
The optimal secondary structure in dot-bracket notation:	(((((((....................)))))))
The centroid secondary structure in dot-bracket notation:	(((((((....................)))))))

The MFE structure

The Centroid structure

The mountain plot representation

Type	Detail	Type	Detail
Aptamer ID	Apta_218	Description	SE15-8min
Aptamer chemistry	RNA	Length	34 nt
GC content	73.5%	Molecular weight	10,959.80 Da
Molarity of 1 μg/μl solution	91.24 μM	Number of G-quadruplexes	3
G-Score	63	Function	Target recognition
Sequence	AGCCGCGAGGGGAGGGAUAGGGUAGGGCGCGGCU
Applications	Specific recognition of various breast cancer cell lines

Type	Detail	Type	Detail
Uniprot ID	P04626	Protein name	Receptor tyrosine-protein kinase erbB-2 (EC 2.7.10.1) (Metastatic lymph node gene 19 protein) (MLN 19) (Proto-oncogene Neu) (Proto-oncogene c-ErbB-2) (Tyrosine kinase-type cell surface receptor HER2) (p185erbB2) (CD antigen CD340)
Gene name(s)	ERBB2 HER2 MLN19 NEU NGL	Organism	Receptor tyrosine-protein kinase erbB-2 (EC 2.7.10.1) (Metastatic lymph node gene 19 protein) (MLN 19) (Proto-oncogene Neu) (Proto-oncogene c-ErbB-2) (Tyrosine kinase-type cell surface receptor HER2) (p185erbB2) (CD antigen CD340)
Status	reviewed in uniprot database	Length	1255
Mass	137,910	Activity regulation	Activated by dimerization
Involvement in disease	Glioma (GLM)	Catalytic activity	Reaction=ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein]
PDB ID(s)	1MFG;1MFL;1MW4;1N8Z;1QR1;1S78;2A91;2JWA;2KS1;2L4K;2N2A;3BE1;3H3B;3MZW;3N85;3PP0;3RCD;3WLW;3WSQ;4GFU;4HRL;4HRM;4HRN;4NND;5K33;5KWG;5MY6;5O4G;5OB4;5TQS;6ATT;6BGT;6J71;6LBX;6OGE;7JXH;7MN5;7MN6;7MN8;
Function	Protein tyrosine kinase that is part of several cell surface receptor complexes, but that apparently needs a coreceptor for ligand binding.

No relevant experimental diagram	Interaction ID	222
	Target type	Protein
	Target unique ID	P04626
	Activity	3.49 nM
	Binding Conditions/Buffer	20 mM HEPES (pH 7.0), 150 mM NaCl, 1 mM MgCl2, 2 mM DTT, and 40 U RNase Inhibitor
	Assay	N/A
	PubMed ID	21749294

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_13	DNA	AGGGGGGGGGGAGGGGTCGGGGTGG	61.76%
Apta_15	DNA	TGAGGGGGGGGGAGGGCGGGGCTGC	61.76%
Apta_706	DNA	CCGGCCAAGGGTGGGAGGGAGGGGGCCGG	61.76%
Apta_1167	RNA	GGCGCGAGGAAGGAGGUCUGAGGAGGUCACUGCGCC	61.11%
Apta_14	DNA	AGCGGGGGGGGCTGGGCTGGGTGGG	58.82%
Apta_19	DNA	TGAGGGGGGGGGAGGTCGGGCCTGC	58.82%
Apta_62	DNA	AGTCCGTGGTAGGGCAGGTTGGGGTGACT	58.82%
Apta_262	DNA	ACGGACTCGCAAAAGGTGGAACAGGAGTGGGCCCCGCGGC	57.50%
Apta_831	DNA	CCGCCCAGCGGGGGTAGGGCCGGACGTAGGAGGAGCTGCG	57.50%
Apta_1013	DNA	ATCACGTATGGGGGGCCGGCATGAGGGCCGCGCGTGACA	56.41%
Apta_590	DNA	ACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCT	56.10%
Apta_666	DNA	TCGACCTCGCGCGAGGAGGGTGGAGGGTCGTAGAGCGCGTA	56.10%
Apta_11	DNA	AGAGGGGGGGGTCGGGGTGGGTCGC	55.88%
Apta_16	DNA	AGGGGGGGGGGACGGGACGGGTATA	55.88%
Apta_17	DNA	AGGGGGGGGGGTGGGGGTGGGTCCC	55.88%
Apta_18	DNA	TGGGGGGTTGGACGGGCGGGGCTGC	55.88%
Apta_20	DNA	AGAGGGGGGGGTGGGGGTGGCCTGC	55.88%
Apta_21	DNA	TGTGGGGGAGGACGGGCGGGGATGC	55.88%
Apta_26	DNA	AGGGGGGGGGGTAAGGGTGGGTAGA	55.88%
Apta_63	DNA	GACCCGTGGTAGGGTAGGATGGGGTGGTC	55.88%

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