Aptamer-protein co-structures (PDB) - amenability precedent

114 experimental aptamer-protein co-structures: demonstrated cases that an aptamer CAN bind a given protein (binding-site precedent). Empirical evidence of aptamer-amenability. Note: aptamers (anionic backbone) strongly favour basic/positive protein interfaces - of 111 computable co-structure interfaces ~103 positive / 5 neutral / 3 negative (preliminary analysis, E. Dohi 2026); acidic/negative epitopes have essentially no electrostatic precedent and are better addressed by small-molecule or modified-aptamer approaches.

Data license: CC BY 4.0 · Data source: apt-scout automated curation pipeline (E. Dohi, NCNP) — values harvested from public databases; raw source stored per target

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Link rowid ▼ pdb_id title keywords resolution_A pmid doi experimental_method
1 1 484D SOLUTION STRUCTURE OF HIV-1 REV PEPTIDE-RNA APTAMER COMPLEX HIV-1 REV PEPTIDE; RNA APTAMER; BOUND PEPTIDE SECONDARY STRUCTURE, PEPTIDE- BINDING RNA, TERTIARY ARCHITECTURES, ADAPTIVE-BINDING, RNA BINDING PROTEIN-RNA COMPLEX       SOLUTION NMR
2 2 9I0V Crystal structure of DasR in complex with a synthetic DasR-binding RNA aptamer Bacterial repressor GntR-HutC family member Synthetic RNA aptamer SELEX-derived aptamer, RNA BINDING PROTEIN 2.02     X-RAY DIFFRACTION
3 3 1EXY SOLUTION STRUCTURE OF HTLV-1 PEPTIDE BOUND TO ITS RNA APTAMER TARGET arginine-guanine sandwich, extended bound basic Rex peptide, flap base, junctional base triplets, RNA binding pocket architecture, RNA BINDING PROTEIN-RNA COMPLEX       SOLUTION NMR
4 4 4PDB CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS RIBOSOMAL PROTEIN S8 IN COMPLEX WITH AN RNA APTAMER PROTEIN-RNA COMPLEX SELEX BASE TRIPLE TRANSLATION, RIBOSOMAL PROTEIN-RNA complex 2.6     X-RAY DIFFRACTION
5 5 6SY4 TetR in complex with the TetR-binding RNA-aptamer K1 TetR, Complex, Aptamer, Transcriptional regulator, DNA BINDING PROTEIN 2.695     X-RAY DIFFRACTION
6 6 3HXO Crystal Structure of Von Willebrand Factor (VWF) A1 Domain in Complex with DNA Aptamer ARC1172, an Inhibitor of VWF-Platelet Binding ARC1779, VWF, Platelet Glycoprotein Ib, Aptamer, ARC1772, Blood coagulation, Cell adhesion, Cleavage on pair of basic residues, Disease mutation, Disulfide bond, Extracellular matrix, Glycoprotein, Hemostasis, Isopeptide bond, Secreted, von Willebrand disease, BLOOD CLOTTING-BLOOD CLOTTING REGULATOR COMPLEX 2.4     X-RAY DIFFRACTION
7 7 3HXQ Crystal Structure of Von Willebrand Factor (VWF) A1 Domain in Complex with DNA Aptamer ARC1172, an Inhibitor of VWF-Platelet Binding ARC1779, VWF, Platelet Glycoprotein Ib, Aptamer, ARC1772, Blood coagulation, Cell adhesion, Cleavage on pair of basic residues, Disease mutation, Disulfide bond, Extracellular matrix, Glycoprotein, Hemostasis, Isopeptide bond, Secreted, von Willebrand disease, BLOOD CLOTTING-BLOOD CLOTTING REGULATOR COMPLEX 2.694     X-RAY DIFFRACTION
8 8 6TXR Structural insights into cubane-modified aptamer recognition of a malaria biomarker Aptamer, Cubamer, PvLDH, DNA 2.5     X-RAY DIFFRACTION
9 9 3EGZ Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch tetracycline, aptamer, riboswitch, antibiotic, RNA 2.2     X-RAY DIFFRACTION
10 10 1ULL RNA APTAMER COMPLEXED WITH HIV-1 REV PEPTIDE, NMR, 7 STRUCTURES REV PEPTIDE-RNA RECOGNITION, ALPHA-HELIX IN WIDENED RNA MAJOR GROOVE, PURINE-PURINE MISMATCHES, UAU BASE TRIPLE, ADAPTIVE BINDING OF PEPTIDE AND RNA IN COMPLEX, COMPLEX (RNA APTAMER-REV PEPTIDE), Viral protein-RNA COMPLEX       SOLUTION NMR
11 11 2RSK RNA aptamer against prion protein in complex with the partial binding peptide Aptamer, Prion, RNA, Alzheimer's disease, Membrane Protein-RNA complex       SOLUTION NMR
12 12 2RU7 Refined structure of RNA aptamer in complex with the partial binding peptide of prion protein Aptamer, Prion, RNA, Alzheimer's disease, Membrane protein-RNA complex       SOLUTION NMR
13 13 9GXH Nanobody bound to TBA G-quadruplex G-quadruplex, DNA, thrombin, nanobody, thrombin-binding aptamer, TBA, IMMUNE SYSTEM 1.9     X-RAY DIFFRACTION
14 14 6DB9 Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer Fluorescent aptamer, Fab, DIR, RNA, RNA-Immune System complex 2.025     X-RAY DIFFRACTION
15 15 6DB8 Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer Fluorescent aptamer, Fab, DIR, RNA, RNA-IMMUNE SYSTEM complex 1.86541345549     X-RAY DIFFRACTION
16 16 3ZH2 Structure of Plasmodium falciparum lactate dehydrogenase in complex with a DNA aptamer OXIDOREDUCTASE 2.1     X-RAY DIFFRACTION
17 17 5HTO Crystal structure of Plasmodium Vivax LDH in complex with a DNA aptamer called pL1 (tetrameric LDH in an asymmetric unit) LDH, malaria, DNA aptamer, aptamer, structural element, OXIDOREDUCTASE-DNA complex 1.9     X-RAY DIFFRACTION
18 18 4M6D Crystal structure of the aptamer minF-lysozyme complex. STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, NYSGRC, PSI-Biology, New York Structural Genomics Research Consortium, Hydrolase-RNA complex 2.68     X-RAY DIFFRACTION
19 19 4Q9Q Crystal structure of an RNA aptamer bound to bromo-ligand analog in complex with Fab G-quadruplex, Fluorescence, Fluorophore, RNA 2.45     X-RAY DIFFRACTION
20 20 4Q9R Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with Fab G-quadruplex, Fluorescence, Fluorophore, RNA-immune system complex 3.12     X-RAY DIFFRACTION
21 21 5HRU Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1 DNA aptamer, Plasmodium LDH, malaria, DNA structural element, OXIDOREDUCTASE-DNA complex 1.71     X-RAY DIFFRACTION
22 22 7SZU Crystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6 fluorogenic, IMMUNE SYSTEM-RNA complex 2.24     X-RAY DIFFRACTION
23 23 1EXD CRYSTAL STRUCTURE OF A TIGHT-BINDING GLUTAMINE TRNA BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASE engineered tRNA, tRNA-protein complex, tRNA aptamer, ligase-RNA COMPLEX 2.7     X-RAY DIFFRACTION
24 24 6MSF F6 APTAMER MS2 COAT PROTEIN COMPLEX VIRAL COAT PROTEIN-RNA COMPLEX, RNA APTAMER, RNA STEM LOOP, BACTERIOPHAGE MS2, Icosahedral virus, Virus-RNA COMPLEX 2.8     X-RAY DIFFRACTION
25 25 7U0Y Crystal structure of Pepper RNA aptamer in complex with HBC599 ligand and Fab BL3-6 fluorogenic RNA, antibody, RNA, IMMUNE SYSTEM-RNA complex 2.66     X-RAY DIFFRACTION
26 26 6SY6 TetR in complex with the TetR-binding RNA-aptamer K2 TetR, transcription regulator, aptamer, RNA, DNA BINDING PROTEIN 2.9     X-RAY DIFFRACTION
27 27 8TFD Crystal structure of a stem-loop DNA aptamer complexed with SARS-CoV-2 nucleocapsid protein RNA-binding domain DNA binding protein, endonuclease, replication, viral protein 1.55     X-RAY DIFFRACTION
28 28 3AHU Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer. Sm-like motif, Protein-RNA complex, TRANSLATION-RNA complex 2.2     X-RAY DIFFRACTION
29 29 3HSB Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer Sm-like motif, Protein-RNA complex, RNA-binding, Stress response, RNA BINDING PROTEIN-RNA COMPLEX 2.2     X-RAY DIFFRACTION
30 30 3V7E Crystal structure of YbxF bound to the SAM-I riboswitch aptamer RNA-protein complex, riboswitch, K-turn, L7Ae-like, A member of the L7Ae/L30e superfamily, Unknown function, K-turn motif, RIBOSOMAL PROTEIN-RNA complex 2.8     X-RAY DIFFRACTION
31 31 5VOE DesGla-XaS195A Bound to Aptamer 11F7t Serine Protease, Blood Coagulation, Aptamer, Inhibitor, HYDROLASE-RNA complex 2.0     X-RAY DIFFRACTION
32 32 5MSF MS2 PROTEIN CAPSID/RNA COMPLEX CAPSID PROTEIN MS2-RNA APTAMER COMPLEX, RNA-PROTEIN COMPLEX, RNA STEM LOOP, BACTERIOPHAGE MS2, Icosahedral virus, Virus-RNA COMPLEX 2.8     X-RAY DIFFRACTION
33 33 7MSF MS2 PROTEIN CAPSID/RNA COMPLEX CCAPSID PROTEIN MS2-RNA APTAMER COMPLEX, RNA-PROTEIN COMPLEX, RNA STEM LOOP, BACTERIOPHAGE MS2, Icosahedral virus, Virus-RNA COMPLEX 2.8     X-RAY DIFFRACTION
34 34 6CF2 Crystal structure of HIV-1 Rev (residues 1-93)-RNA aptamer complex HIV-1, Rev, RNA aptamer, RNA BINDING PROTEIN-RNA complex 3.0     X-RAY DIFFRACTION
35 35 3UZT Structure of the C13.18 RNA Aptamer in Complex with G Protein-Coupled Receptor Kinase 2 Protein-RNA complex, Protein Kinase Fold, RGS Homology Domain, Pleckstrin Homology Domain, G Protein-Coupled Receptor Phosphorylation, RNA Aptamer, TRANSFERASE-RNA complex 3.51     X-RAY DIFFRACTION
36 36 4M4O Crystal structure of the aptamer minE-lysozyme complex STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, NYSGRC, protein-RNA complex, PSI-Biology, New York Structural Genomics Research Consortium, HYDROLASE-RNA complex 2.0     X-RAY DIFFRACTION
37 37 8ZBF Crystal structure of the A58-T10 DNA aptamer in complex with SARS-CoV-2 N-NTD aptamer, A58, nucleocapsid protein, SARS-CoV-2, DNA 2.8     X-RAY DIFFRACTION
38 38 4WB2 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a complement anaphylatoxin protein-RNA complex, mirror-image aptamer, G-quadruplex, complement anaphylatoxin, DNA-RNA hybrid 1.8     X-RAY DIFFRACTION
39 39 4WB3 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin protein-RNA complex, mirror-image aptamer, G-quadruplex, complement anaphylatoxin, DNA-RNA hybrid 2.0     X-RAY DIFFRACTION
40 40 7V5N Crystal structure of Fab fragment of bevacizumab bound to DNA aptamer antibody, DNA complex, DNA BINDING PROTEIN, IMMUNE SYSTEM-DNA complex 1.7     X-RAY DIFFRACTION
41 41 6B14 Crystal structure of Spinach RNA aptamer in complex with Fab BL3-6S97N Spinach RNA aptamer, Antibody engineering, Chaperone-assisted RNA crystallography, immune system-rna complex 1.64     X-RAY DIFFRACTION
42 42 7F49 von Willebrand factor (VWF) A1 domain with BT-100 aptamer RNA aptamers, arterial thrombosis, platelets, primates, von Willebrand factor, BLOOD CLOTTING 2.09     X-RAY DIFFRACTION
43 43 7YQ6 human insulin receptor bound with A62 DNA aptamer receptor-ligand complex_C, STRUCTURAL PROTEIN 4.18     ELECTRON MICROSCOPY
44 44 6B3K Crystal structure of mutant Spinach RNA aptamer in complex with Fab BL3-6 RNA aptamer, Fragment of antibody, Chaperone-assisted RNA Crystallography, immune system-rna complex 2.09     X-RAY DIFFRACTION
45 45 8DK7 Crystal structure of theophylline aptamer soaked with TAL2 RNA, aptamer, theophylline, RNA-IMMUNE SYSTEM complex 2.46     X-RAY DIFFRACTION
46 46 8EPK Complex of anticoagulant RNA aptamer and human coagulation factor IXa (S195A) coagulation factor IX, RNA aptamer, inhibitor, BLOOD CLOTTING 2.65     X-RAY DIFFRACTION
47 47 3UCU The c-di-GMP-I riboswitch bound to pGpG riboswitch, SIGNALING PROTEIN-RNA complex 2.8     X-RAY DIFFRACTION
48 48 3UCZ The c-di-GMP-I riboswitch bound to GpG riboswitch, SIGNALING PROTEIN-RNA complex 2.8     X-RAY DIFFRACTION
49 49 3UD3 The C92U mutant c-di-GMP-I riboswitch bound to pGpA riboswitch, SIGNALING PROTEIN-RNA complex 3.1     X-RAY DIFFRACTION
50 50 3UD4 The C92U mutant c-di-GMP-I riboswitch bound to GpA riboswitch, SIGNALING PROTEIN-RNA complex 2.7     X-RAY DIFFRACTION

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CREATE TABLE aptamer_costructures (pdb_id TEXT, title TEXT, keywords TEXT, resolution_A TEXT, pmid TEXT, doi TEXT, experimental_method TEXT);