Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 215
Aptamer sequence: GGTTGGTGTGGTTGG
Target unique ID: P04585
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_211 TBA (thrombin aptamer) Protein POL_HV1H2 > 750 nM 50 mM Tris-HCl, pH 8, 1mM DTT, 80 mM KCl, 6 mM MgCl2 for ten minutes 22554064
Structure information of aptamer
Aptamer Sequence: GGTTGGTGTGGTTGG
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
Aptamer information
Type Detail Type Detail
Aptamer ID Apta_211 Description TBA (thrombin aptamer)
Aptamer chemistry DNA Length 15 nt
GC content 60.0% Molecular weight 4,965.99 Da
Molarity of 1 μg/μl solution 201.37 μM Number of G-quadruplexes 2
G-Score 20 Function Targeted binding
Sequence GGTTGGTGTGGTTGG
Applications Binds specifically to thrombin
Target information
Type Detail Type Detail
Uniprot ID P04585 Protein name Gag-Pol polyprotein (Pr160Gag-Pol) [Cleaved into: Matrix protein p17 (MA); Capsid protein p24 (CA); Spacer peptide 1 (SP1) (p2); Nucleocapsid protein p7 (NC); Transframe peptide (TF); p6-pol (p6*); Protease (EC 3.4.23.16) (PR) (Retropepsin); Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.13) (Exoribonuclease H) (EC 3.1.13.2) (p66 RT); p51 RT; p15; Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)]
Gene name(s) gag-pol Organism Gag-Pol polyprotein (Pr160Gag-Pol) [Cleaved into: Matrix protein p17 (MA); Capsid protein p24 (CA); Spacer peptide 1 (SP1) (p2); Nucleocapsid protein p7 (NC); Transframe peptide (TF); p6-pol (p6*); Protease (EC 3.4.23.16) (PR) (Retropepsin); Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.13) (Exoribonuclease H) (EC 3.1.13.2) (p66 RT); p51 RT; p15; Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)]
Status reviewed in uniprot database Length 1435
Mass 162,042 Activity regulation The viral protease is inhibited by many synthetic protease inhibitors (PIs), such as amprenavir, atazanavir, indinavir, loprinavir, nelfinavir, ritonavir and saquinavir
Involvement in disease N/A Catalytic activity Reaction=Specific for a P1 residue that is hydrophobic, and P1' variable
PDB ID(s)
1A30;1BV7;1BV9;1BVE;1BVG;1BWA;1BWB;1C0T;1C0U;1C1B;1C1C;1DMP;1DTQ;1DTT;1E6J;1EP4;1ESK;1EX4;1EXQ;1FB7;1FK9;1FKO;1FKP;1G6L;1HIV;1HVH;1HVR;1HWR;1HXB;1JKH;1JLA;1JLB;1JLC;1JLE;1JLF;1JLG;1JLQ;1KLM;1LV1;1LW0;1LW2;1LWC;1LWE;1LWF;1NCP;1O1W;1ODW;1ODY;1QBR;1QBS;1QBT;1QBU;1REV;1RT1;1RT2;1RT3;1RT4;1RT5;1RT6;1RT7;1RTD;1RTH;1RTI;1RTJ;1S1T;1S1U;1S1V;1S1W;1S1X;1T05;1TAM;1TKT;1TKX;1TKZ;1TL1;1TL3;1VRT;1VRU;2HND;2HNY;2HNZ;2KOD;2NPH;2OPP;2OPQ;2OPR;2OPS;2RF2;2RKI;2WHH;2WOM;2WON;2YNF;2YNG;2YNH;2YNI;3AO2;3C6T;3C6U;3DI6;3DLE;3DLG;3DM2;3DMJ;3DOK;3DOL;3DOX;3DRP;3DRR;3DRS;3DYA;3E01;3FFI;3I0R;3I0S;3KJV;3KK1;3KK2;3KK3;3KT2;3KT5;3LAK;3LAL;3LAM;3LAN;3LP0;3LP1;3LP2;3M8P;3M8Q;3MEC;3MED;3MEE;3MEG;3N3I;3NBP;3PHV;3QIN;3QIO;3QIP;3T19;3T1A;3TAM;4B3O;4B3P;4B3Q;4I7F;4KSE;4KV8;4NCG;4Q1W;4Q1X;4Q1Y;4Q5M;4QLH;4U1H;4U1I;4U1J;4U7Q;4U7V;5DGU;5DGW;5EU7;5HRN;5HRP;5HRR;5HRS;5IM7;5J2M;5J2N;5J2P;5J2Q;5K14;5KAO;5T82;5TC2;5VZ6;5XOS;5XOT;5YRS;6BJ2;6BJ3;6BSG;6BSH;6BSI;6BSJ;6DIF;6DIL;6DJ1;6DJ2;6DJ5;6DJ7;6DV0;6DV4;6E7J;6E9A;6EWA;6EX9;6GL1;6J1V;6J1W;6OR7;6OTZ;6P1I;6P1X;6P2G;6PYL;6SKK;6SKM;6SKN;6SLQ;6SLU;6SMU;6UIR;6UIS;6UIT;6UJX;6UJY;6UJZ;6UK0;6VPZ;6VQ2;6VQD;6VQE;6VQY;6VQZ;6WAZ;6WB1;6WPF;6WPH;6WPJ;
Function Mediates, with Gag polyprotein, the essential events in virion assembly, including binding the plasma membrane.
Activity data

No relevant experimental diagram

 Interaction ID 78
Target type Protein
Target unique ID P00734
Activity 25 nM
Binding Conditions/Buffer

50 mM HEPES, 100 mM NaCl, 1 mM MgCl2, 5 mM KCl, 1 mM,CaCl2, pH 7.4
Assay

N/A
PubMed ID 31580650

No relevant experimental diagram

 Interaction ID 215
Target type Protein
Target unique ID P04585
Activity > 750 nM
Binding Conditions/Buffer

50 mM Tris-HCl, pH 8, 1mM DTT, 80 mM KCl, 6 mM MgCl2 for ten minutes
Assay

N/A
PubMed ID 22554064
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_210 DNA AGGTTGGTTGGTTGGAAT 72.22%
Apta_757 DNA GGTGGTGGTGGTTGTGGTGGTGG 65.22%
Apta_545 DNA TTAGTTGGGGTTCAGTTGG 63.16%
Apta_198 DNA AGGAAGGCTTTAGGTCTGAG 60.00%
Apta_806 DNA GGTTGGATGTAAGGTTGGAGGGGGG 60.00%
Apta_1196 DNA GGGGGATGGGGG 60.00%
Apta_1197 DNA GGGGGCATGGGGG 60.00%
Apta_1038 DNA CCCGTCCGTATGGTGGG 58.82%
Apta_1039 DNA GCCCGTCCGTATGGTGGGT 57.89%
Apta_350 DNA GGTGGTGGTGGTTGTGGTGGTGGTGG 57.69%
Apta_546 DNA CACGGCATGGTGGGCGTCGTG 57.14%
Apta_197 DNA GGCTTTAGGTCTGAGATCTCGGAAT 56.00%
Apta_539 DNA CGTGTTGTCTCTCTGTGTCTCG 54.55%
Apta_389 DNA GCCTGTGGTGTTGGGGCGGGTGCG 54.17%
Apta_390 DNA GGTGCGGCGGGACTAGTGGGTGTG 54.17%
Apta_203 DNA GGAAGGCTTTAGGTCTGAGATCTCGG 53.85%
Apta_1193 DNA GGGTTGGAGGTGGAGGGGAGTTGAGG 53.85%
Apta_147 DNA TGCGGTTGTAGTACTCGTGGCCG 52.17%
Apta_12 DNA TGAGGGGGTGGGTGGGACGGGTTGG 52.00%
Apta_1086 DNA GCAGTTGATCCTTTGGATACCCTGG 52.00%

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AptaDB is an online database we developed to integrate comprehensive information about aptamer.
The detail of this database is described here:

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