Table 2.
The structural and affinity characteristics of aptamer–protein complexes.
| PDB ID | Complex Type (Protein:mAptamer) | Polar Contacts (Number) | Interface Area (A2) | Dissociation Constant (nm) | Gibbs Free Energy Change (kJ/mol) | References |
|---|---|---|---|---|---|---|
| 5mxf | Photorhabdus asymbiotica lectin (PHL): alpha-methyl fucoside | 16 | 1165.2 | 1.4 ± 0.21 μm | −48.8 | [32] |
| 1u1y | MS2 coat protein: F5 RNA aptamer | 42 | 3180.6 | 0.6 ± 0.3 | −51.2 | [33] |
| 1exd | Glutamine aminoacyl tRNA synthetase: Glutamine tRNA | 42 | 2599.3 | 0.3 ± 0.1 | −35.9 | [34] |
| 1ooa | NF-kB(p50)2: RNA Aptamer | 27 | 1343.1 | 5.4 ± 2.2 | 0.1 | [35] |
| 2b63 | Complete RNA Polymerase II: RNA inhibitor | 147 | 9311.5 | 33 ± 2 | −91.8 | [36] |
| 4i7y | Human Alpha Thrombin: 27-mer DNA Aptamer | 18 | 1079.5 | 0.7 | −6.1 | [37] |
| 5ew1 | Human thrombin: two DNA aptamers (HD22 and HD1-ΔT3) | 21 | 1116.2 | 4.9 ± 1.6 51.8 ± 5.3 |
−10.0 | [38,39] |
| 4dii | Human alpha thrombin: thrombin binding DNA aptamer | 32 | 1086.0 | 33 | −9.4 | [40,41] |
| 3agv | Human IgG: RNA aptamer | 13 | 1092.0 | - | −12.8 | [42,43] |
| 3qlp | Human alpha thrombin: modified thrombin binding DNA aptamer | 39 | 1404.0 | 25 ± 1 | −9.5 | [41,44] |
| 3hxq | Von Willebrand Factor (VWF) A1 Domain: DNA Aptamer ARC1172 | 23 | 1070.8 | 2 | −1.2 | [45,46] |
| 3uzs | G Protein-Coupled Receptor Kinase 2-Heterotrimeric G Protein Beta 1 and Gamma 2 Subunit Complex: C13.28 RNA Aptamer | 13 | 2188.7 | 3.8 ± 1.2 | −41.7 | [47] |
| 3uzt | G Protein-Coupled Receptor Kinase 2: C13.18 RNA Aptamer | 8 | 1096.8 | 35 ± 5 | −4.2 | [47] |
| 4hqx | Human PDGF-BB: Modified DNA aptamer (SOMAmer SL4) | 24 | 1076.8 | 1.20 | −14.4 | [48] |
| 4hqu | Human PDGF-BB: Modified DNA aptamer (SOMAmer SL5) | 24 | 1078.6 | 0.02 | −14.9 | [48] |
| 4lz4 | Human thrombin: TBA (DNA) deletion mutant lacking thymine 3 nucleobase | 43 | 1354.5 | 54.9 | −10.6 | [49] |
| 5hto | Plasmodium Vivax LDH: DNA aptamer pL1 | 14 | 2105.1 | 16.8 ± 0.6 | −37.3 | [50] |
| 4wb2 | Mouse C5a complement anaphylatoxin: mirror-image L-RNA/L-DNA aptamer NOX-D20 | 14 | 420.6 | 0.02 | −3.1 | [51] |
| 3zh2 | Plasmodium falciparum lactate dehydrogenase: DNA aptamer | 13 | 2106.3 | 42 | −37.6 | [52] |
| 4pdb | Bacillus Anthracis Ribosomal Protein S8: RNA Aptamer | 13 | 898.6 | 110 ± 30 | −16.7 | [5] |
| 4ni7 | Human interleukin 6: a modified DNA aptamer (SOMAmer SL1025) | 3 | 336.3 | 0.20 | 3.0 | [53] |
| 4r8i | Chemokine CCL2: Mirror-image RNA Oligonucleotide Aptamer | 10 | 807.3 | 1.4 ± 0.16 | −8.8 | [54] |
| 4zbn | Nerve growth factor: non-helical DNA triplex aptamer | 13 | 1418.9 | 0.21 ± 0.08 | −25.2 | [55] |
| 5cmx | Human alpha thrombin: duplex/quadruplex DNA aptamer | 32 | 1124.0 | 0.56 | −9.0 | [56] |
| 5hrt | Mouse autotaxin: DNA aptamer | 8 | 934.6 | 1.6 | −11.7 | [57] |
| 5do4 | Thrombin: RNA aptamer | 31 | 1173.1 | 0.0081 ± 0.0002 | −8.6 | [58] |
| 5uc6 | IL-1 alpha: naphthyl-modified DNA aptamer | 4 | 598.4 | 7.3 | −1.1 | [59] |
| 6eo6 | Human alpha-thrombin: modified 15-mer DNA aptamer | 36 | 1064.1 | 1.00 | −7.9 | [60] |
| 6sy4 | TetR: TetR-binding RNA-aptamer K1 | 8 | 1615.2 | 5.6 | −31.2 | [61] |
| 6rti | Human glutamate carboxypeptidase II: aptamer A9g | 24 | 2414.7 | - | −25.8 | [62] |
| 6z8w | Human alpha thrombin: thrombin binding aptamer variant (TBA-3G) | 34 | 1066.1 | 9.8 ± 0.6 | −8.1 | [63] |
| 7jtq | Human complement factor B: Slow off-rate modified aptamer | 10 | 894.9 | 0.049 | −3.1 | [64] |