IMB Jena Image Library of Biological Macromolecules (Last update: November 15, 2004) ----------------------------------------------------------------- Comprehensive Bending Classification of Nucleic Acid Double Helix Structures ----------------------------------------------------------------- Table 2c: Structures for which the helical axis is best described by a double-kink line. Sigma2 of a double-kink line is only slightly smaller (<0.2) than for the next best model(s). The structures are listed by the number of base pairs (bp). Number of structures: 92 PDB NDB bp molecule method helical s(2) r a/a1 a2 a1+a2 o l1 l2 l3 type axes shape 1b69 ------ 13 prot-nuc NMR double-kink 0.509 11 27 38 77 3 6 4 single-kink 0.553 28 9 4 1efs ------ 13 nuc NMR double-kink 0.042 8 4 12 113 4 4 5 single-kink 0.061 7 4 9 circular 0.073 249 straight 0.143 1j1v pd0371 13 prot-nuc diff double-kink 0.226 14 15 29 53 3 5 5 circular 0.277 72 single-kink 0.346 18 7 6 1j59 pd0299 13 prot-nuc diff double-kink 0.372 15 32 47 33 5 4 4 circular 0.494 38 single-kink 0.494 38 8 5 1nk5 pd0378 13 prot-nuc diff double-kink 0.270 18 14 32 -137 4 2 7 circular 0.379 130 single-kink 0.428 10 5 8 1nkb pd0383 13 prot-nuc diff double-kink 0.228 28 15 43 102 6 4 3 single-kink 0.312 27 6 7 1qln ph0002 13 prot-nuc diff double-kink 0.310 13 12 25 84 4 6 3 circular 0.317 99 single-kink 0.405 13 6 7 6gat ------ 13 prot-nuc NMR double-kink 0.058 10 13 23 -33 5 3 5 circular 0.102 76 single-kink 0.116 19 7 6 1ahd ------ 14 prot-nuc NMR double-kink 0.412 25 12 37 -76 5 3 6 single-kink 0.461 29 6 8 circular 0.580 51 1bwg ------ 14 nuc NMR double-kink 0.155 15 8 23 -147 4 6 4 single-kink 0.197 14 3 11 1cqt pd0092 14 prot-nuc diff double-kink 0.533 12 25 37 -92 4 5 4 single-kink 0.707 23 9 5 1ecr pdte01 14 prot-nuc diff double-kink 0.243 22 13 35 -92 5 6 3 single-kink 0.346 22 5 9 1j46 ------ 14 prot-nuc NMR double-kink 0.278 13 34 47 4 4 5 5 single-kink 0.291 40 8 6 circular 0.335 38 1jey pd0220 14 prot-nuc diff double-kink 0.155 13 13 26 96 7 4 3 single-kink 0.236 14 7 7 circular 0.286 103 1k8j ------ 14 nuc NMR double-kink 0.174 11 12 23 147 2 9 3 single-kink 0.210 10 11 2 straight 0.233 circular 0.274 733 1k9h ------ 14 nuc NMR double-kink 0.086 12 15 27 -51 4 4 6 single-kink 0.165 20 7 7 circular 0.177 62 1mdy pdt016 14 prot-nuc diff double-kink 0.266 16 16 32 110 6 2 6 single-kink 0.310 18 7 7 circular 0.421 84 9ant pd0007 14 prot-nuc diff double-kink 0.220 22 13 35 -106 6 2 6 single-kink 0.327 21 6 8 1cf7 pd0045 15 prot-nuc diff double-kink 0.239 7 10 17 -91 4 4 6 single-kink 0.261 10 9 6 circular 0.276 158 1drg pd0113 15 prot-nuc diff double-kink 0.272 18 16 34 -48 7 3 5 single-kink 0.287 28 8 7 1dsz pd0115 15 prot-nuc diff double-kink 0.200 11 7 18 -163 5 6 4 single-kink 0.224 9 4 10 circular 0.363 349 straight 0.399 1lq1 pd0314 15 prot-nuc diff double-kink 0.113 14 15 29 -40 6 3 6 circular 0.129 62 single-kink 0.193 24 8 7 1lwa ------ 15 nuc NMR double-kink 0.468 23 20 43 60 3 9 3 circular 0.655 108 1pue pdt033 15 prot-nuc diff double-kink 0.185 27 12 39 -124 7 4 4 single-kink 0.303 24 7 8 2lef ------ 15 prot-nuc NMR double-kink 0.407 37 30 67 -28 5 4 6 circular 0.590 26 1g4d ------ 16 prot-nuc NMR double-kink 0.117 14 10 24 98 4 4 8 circular 0.275 141 1lei pd0310 16 prot-nuc diff double-kink 0.144 17 14 31 -14 5 5 6 circular 0.196 64 single-kink 0.295 25 7 9 1ma7 pd0337 16 prot-nuc diff double-kink 0.289 20 18 38 30 7 3 6 single-kink 0.316 34 8 8 1n4l pd0359 16 prot-nuc diff double-kink 0.043 12 10 22 -87 5 7 4 circular 0.226 161 single-kink 0.229 12 5 11 1saa ------ 16 nuc NMR double-kink 0.113 15 14 29 -48 6 5 5 circular 0.145 84 1zme pdt044 16 prot-nuc diff double-kink 0.408 26 21 47 -38 7 3 6 single-kink 0.479 42 8 8 circular 0.534 38 2gat ------ 16 prot-nuc NMR double-kink 0.097 16 8 24 83 3 9 4 single-kink 0.248 12 4 12 circular 0.272 248 3gat ------ 16 prot-nuc NMR double-kink 0.130 12 16 28 90 2 12 2 straight 0.282 2crx pd0103 17 prot-nuc diff double-kink 0.334 26 12 38 -30 8 4 5 single-kink 0.371 33 9 8 circular 0.499 51 2stw ------ 17 prot-nuc NMR double-kink 0.266 28 10 38 -68 7 7 2 single-kink 0.282 29 7 10 3crx pd0104 17 prot-nuc diff double-kink 0.317 17 20 37 -11 7 3 7 single-kink 0.387 34 8 9 1ign pdt035 18 prot-nuc diff double-kink 0.259 22 9 31 86 9 3 6 single-kink 0.315 23 9 9 1j5o pd0316 18 prot-nuc diff double-kink 0.807 31 18 49 25 5 6 7 circular 0.904 52 1k3w pd0253 18 prot-nuc diff double-kink 0.218 19 30 49 2 5 4 9 single-kink 0.328 42 8 10 1kb2 pd0268 18 prot-nuc diff double-kink 0.252 9 7 16 -159 7 2 8 single-kink 0.258 3 7 11 circular 0.267 724 straight 0.275 1kb4 pd0269 18 prot-nuc diff double-kink 0.209 9 10 19 170 7 5 5 straight 0.406 1kb6 pd0270 18 prot-nuc diff double-kink 0.227 8 10 18 -162 7 5 6 single-kink 0.367 5 13 4 straight 0.376 1ksx pd0282 18 prot-nuc diff double-kink 0.111 12 12 24 76 3 12 3 circular 0.229 370 single-kink 0.239 13 3 15 1lat pdt030 18 prot-nuc diff double-kink 0.289 9 7 16 -173 7 4 7 single-kink 0.317 5 5 13 straight 0.336 circular 0.363 968 1mm8 pd0340 18 prot-nuc diff double-kink 0.261 31 16 47 -2 6 3 9 single-kink 0.310 44 7 11 1muh pd0347 18 prot-nuc diff double-kink 0.212 29 19 48 0 6 3 9 single-kink 0.253 45 7 11 1mur pd0349 18 prot-nuc diff double-kink 0.218 19 30 49 2 5 4 9 single-kink 0.328 42 8 10 1mus pd0350 18 prot-nuc diff double-kink 0.209 29 18 47 5 6 3 9 single-kink 0.261 44 7 11 1nkp pd0386 18 prot-nuc diff double-kink 0.176 11 14 25 -161 4 6 8 single-kink 0.277 11 11 7 1nlw pd0387 18 prot-nuc diff double-kink 0.153 9 6 15 -1 4 6 8 circular 0.170 183 single-kink 0.185 10 7 11 1qar ------ 18 prot-nuc model double-kink 0.144 18 15 33 -54 6 6 6 circular 0.334 77 2dgc pdt029 18 prot-nuc diff double-kink 0.099 12 12 24 78 6 6 6 circular 0.277 120 2nll pdr021 18 prot-nuc diff double-kink 0.394 9 9 18 -97 5 6 6 circular 0.440 212 single-kink 0.530 8 10 8 1puf pd0455 19 prot-nuc diff double-kink 0.191 11 12 23 140 10 4 5 single-kink 0.345 8 9 10 2hap pd0090 19 prot-nuc diff double-kink 0.406 25 10 35 125 7 8 4 single-kink 0.506 24 7 12 3cro pdr001 19 prot-nuc diff double-kink 0.145 18 18 36 -20 6 8 5 circular 0.271 83 1a73 pd0002 20 prot-nuc diff double-kink 0.238 33 30 63 -18 9 2 9 single-kink 0.274 61 10 10 1a74 pde140 20 prot-nuc diff double-kink 0.237 33 31 64 -27 9 2 9 single-kink 0.302 61 10 10 1apl pdt005 20 prot-nuc diff double-kink 0.193 10 9 19 -94 5 6 9 circular 0.368 195 single-kink 0.392 10 10 10 1awc pdt048 20 prot-nuc diff double-kink 0.214 13 8 21 121 9 3 7 single-kink 0.301 11 8 11 circular 0.401 195 1cyq pd0096 20 prot-nuc diff double-kink 0.291 35 31 66 -30 9 2 9 single-kink 0.366 62 10 10 1cz0 pd0097 20 prot-nuc diff double-kink 0.259 34 31 65 -23 9 2 9 single-kink 0.303 62 10 10 1du0 pd0114 20 prot-nuc diff double-kink 0.185 11 10 21 124 8 7 5 single-kink 0.367 10 7 13 1ga5 pd0191 20 prot-nuc diff double-kink 0.377 11 11 22 -154 8 5 7 single-kink 0.554 10 5 15 1hlz pd0193 20 prot-nuc diff double-kink 0.385 13 9 22 -164 8 6 6 single-kink 0.459 13 5 15 1i3j pd0200 20 prot-nuc diff double-kink 0.145 9 16 25 173 6 4 10 single-kink 0.217 11 11 9 1ipp pde0144 20 prot-nuc diff double-kink 0.311 62 12 74 -117 10 7 3 single-kink 0.318 62 10 10 1n5y pd0365 20 prot-nuc diff double-kink 0.228 20 11 31 -31 6 6 8 single-kink 0.353 25 8 12 1n6q pd0364 20 prot-nuc diff double-kink 0.229 20 8 28 -34 8 5 7 single-kink 0.301 24 9 11 circular 0.352 80 1nwq pd0395 20 prot-nuc diff double-kink 0.318 15 12 27 -117 10 5 5 single-kink 0.455 13 9 11 circular 0.460 149 1qp9 pd0148 20 prot-nuc diff double-kink 0.400 22 10 32 98 8 8 4 single-kink 0.464 22 8 12 2hdd pdt043 20 prot-nuc diff double-kink 0.138 7 13 20 148 8 7 5 single-kink 0.316 10 15 5 1f4k pd0167 21 prot-nuc diff double-kink 0.124 11 11 22 -2 4 12 5 circular 0.135 200 single-kink 0.291 10 12 9 1ksy pd0283 21 prot-nuc diff double-kink 0.151 7 7 14 -175 9 3 9 straight 0.197 single-kink 0.212 2 16 5 circular 0.223 >1000 1p47 pd0424 21 prot-nuc diff double-kink 0.286 7 12 19 -156 6 7 8 single-kink 0.340 10 15 6 1par pdr012 21 prot-nuc diff double-kink 0.489 22 11 33 -30 8 6 7 circular 0.504 78 single-kink 0.585 27 10 11 1rep pd0107 21 prot-nuc diff double-kink 0.276 9 18 27 26 5 6 10 single-kink 0.312 22 10 11 circular 0.313 96 1rtd pd0023 21 prot-nuc diff double-kink 0.160 15 11 26 30 7 7 7 circular 0.184 107 1a36 pde0141 22 prot-nuc diff double-kink 0.096 5 7 12 148 3 13 6 single-kink 0.100 7 17 5 circular 0.184 667 straight 0.263 1an2 pdt023 22 prot-nuc diff double-kink 0.332 9 8 17 170 7 3 12 straight 0.371 single-kink 0.385 2 11 11 circular 0.401 >1000 1ej9 pd0125 22 prot-nuc diff double-kink 0.067 7 6 13 -166 7 6 9 straight 0.229 circular 0.230 >1000 single-kink 0.238 3 6 16 1hf0 pd0274 22 prot-nuc diff double-kink 0.417 6 17 23 -58 6 12 3 circular 0.449 329 single-kink 0.555 8 7 15 1juw ------ 22 prot-nuc model double-kink 0.096 5 7 12 148 3 13 6 single-kink 0.100 7 17 5 circular 0.184 667 straight 0.263 1lpq pd0313 22 prot-nuc diff double-kink 0.041 2 4 6 -137 12 5 4 single-kink 0.043 3 18 4 straight 0.053 circular 0.060 >1000 1g9y pd0189 24 prot-nuc diff double-kink 0.702 28 22 50 -21 7 10 7 circular 0.706 74 1mey pdtb41 24 prot-nuc diff double-kink 0.720 11 17 28 -61 7 7 10 circular 0.859 113 6pax pd0050 24 prot-nuc diff double-kink 0.211 20 5 25 -129 10 3 10 single-kink 0.226 18 10 14 1k78 pd0259 25 prot-nuc diff double-kink 0.252 10 10 20 -137 10 3 12 circular 0.387 348 single-kink 0.414 7 13 12 1jt0 pd0249 28 prot-nuc diff double-kink 0.777 12 13 25 -46 4 20 4 circular 0.832 511 1tf6 pdt065 30 prot-nuc diff double-kink 1.040 12 12 24 4 17 5 7 single-kink 1.040 21 19 11 1gfx ------ 43 prot-nuc model double-kink 1.718 20 21 41 -10 13 15 15 circular 1.814 143 1j5g ------ 43 prot-nuc model double-kink 1.713 20 21 41 -10 13 15 15 circular 1.809 143 -------------------------------------------------------------------------- Abbreviations -------------------------------------------------------------------------- PDB Protein Data Bank NDB Nucleic Acid Database bp base pair number diff diffraction model theoretical model NMR nuclear magnetic resonance spectroscopy prot protein nuc nucleic acid prot-nuc protein-nucleic acid complex carb carbohydrate plane plane s(2) goodness of fit r radius of curvature (circular line) a kink angle (single-kink line) a1, a2 kink angles (double-kink line) o twist angle (double-kink line) l1, l2, l3 lenght of segments 1, 2, and 3 measured in bp (double-kink model)