IMB Jena Image Library of Biological Macromolecules (last update: November 15, 2004) ----------------------------------------------------------------- Comprehensive Bending Classification of Nucleic Acid Double Helix Structures No bending (M = 0°) Classification I = Classification II (There are structures with 13 or more base pairs for which a double-kink helical axis is selected as the most appropriate description by the automatic approach, but the central segment consists of 0 or 1 base pairs only. In these cases the double-kink geometrical parameters make no sense. Therefore, these structures have to be viewed as single-kink structures. They are indicated by a * in the model description). ----------------------------------------------------------------- Number of structures: 313 + 9 PDB NDB bp molecule method helical s(2) r a/a2 a2 a1+a2 M type axis shape 110d ddf039 6 nuc diff straight 0.676 0 146d ------ 6 nuc NMR straight 0.180 0 151d ddf044 6 nuc diff straight 0.430 0 152d ddf045 6 nuc diff straight 0.391 0 182d ddf049 6 nuc diff straight 0.164 0 185d ------ 6 nuc NMR straight 0.470 0 198d ddf050 6 nuc diff straight 0.329 0 1agl ddf072 6 nuc diff straight 0.327 0 1ao1 ------ 6 nuc NMR straight 0.494 0 1bcb ------ 6 nuc NMR straight 0.098 0 1bce ------ 6 nuc NMR straight 0.049 0 1buf ------ 6 nuc NMR straight 0.091 0 1c9z dd0018 6 nuc diff straight 0.359 0 1cx3 ------ 6 nuc NMR straight 0.264 0 1d10 ddf020 6 nuc diff straight 0.422 0 1d11 ddf001 6 nuc diff straight 0.395 0 1d12 ddf019 6 nuc diff straight 0.405 0 1d14 ddfp21 6 nuc diff straight 0.486 0 1d15 ddf022 6 nuc diff straight 0.407 0 1d17 ddfa16 6 nuc diff straight 0.107 0 1d1u pd0152 6 prot-nuc diff straight 0.125 0 1d21 ddfa14 6 nuc diff straight 0.105 0 1d22 ddfa15 6 nuc diff straight 0.143 0 1d33 ddf023 6 nuc diff straight 0.455 0 1d35 ddfb25 6 nuc diff straight 0.455 0 1d36 ddf026 6 nuc diff straight 0.354 0 1d37 ddf028 6 nuc diff straight 0.248 0 1d38 ddf029 6 nuc diff straight 0.442 0 1d3r bd0017 6 nuc diff straight 0.263 0 1d54 ddf035 6 nuc diff straight 0.634 0 1d58 ddf036 6 nuc diff straight 0.467 0 1d67 ddf038 6 nuc diff straight 0.366 0 1d97 bdfp24 6 nuc diff straight 0.320 0 1da0 ddf018 6 nuc diff straight 0.639 0 1da9 ddf040 6 nuc diff straight 0.865 0 1dl8 dd0023 6 nuc diff straight 0.196 0 1em0 dd0027 6 nuc diff straight 0.276 0 1f69 bd0039 6 nuc diff straight 0.142 0 1f6c bd0040 6 nuc diff straight 0.136 0 1g00 ad0010 6 nuc diff straight 0.163 0 1g5k ------ 6 nuc NMR straight 0.231 0 1gj1 ------ 6 nuc NMR straight 0.112 0 1i5v ------ 6 nuc NMR straight 1.326 0 1i6j pd0202 6 prot-nuc diff straight 0.206 0 1i7j ar0031 6 nuc diff straight 0.147 0 1ih1 bd0050 6 nuc diff straight 0.189 0 1ih2 ad0021 6 nuc diff straight 0.259 0 1ih3 ad0022 6 nuc diff straight 0.147 0 1ih4 ad0023 6 nuc diff straight 0.234 0 1ih6 ad0024 6 nuc diff straight 0.366 0 1imr ddf061 6 nuc diff straight 0.370 0 1ims ddf062 6 nuc diff straight 0.393 0 1ixy pd0333 6 prot-nuc diff straight 0.127 0 1j7t dr0006 6 nuc diff straight 1.360 0 1k2j ------ 6 nuc NMR straight 0.303 0 1k2k ------ 6 nuc NMR straight 0.276 0 1k82 pd0264 6 prot-nuc diff straight 0.209 0 1k9g dd0047 6 nuc diff straight 0.126 0 1kci dd0048 6 nuc diff straight 0.271 0 1kfv pd0277 6 prot-nuc diff straight 0.067 0 1l1t pd0292 6 prot-nuc diff straight 0.247 0 1l1z pd0293 6 prot-nuc diff straight 0.185 0 1l2b pd0294 6 prot-nuc diff straight 0.128 0 1l2c pd0295 6 prot-nuc diff straight 1.543 0 1l2d pd0296 6 prot-nuc diff straight 0.859 0 1l3z ar0040 6 nuc diff straight 0.169 0 1m0e pd0327 6 prot-nuc diff straight 0.174 0 1m5r pd0334 6 prot-nuc diff straight 0.108 0 1msw pd0345 6 prot-nuc diff straight 0.379 0 1mtg ------ 6 nuc NMR straight 0.179 0 1n0k ------ 6 nuc NMR straight 0.897 0 1n0o ------ 6 nuc NMR straight 0.062 0 1nab dd0054 6 nuc diff straight 0.887 0 1p20 dd0056 6 nuc diff straight 0.434 0 1p24 bd0063 6 nuc diff straight 0.371 0 1p25 bd0064 6 nuc diff straight 0.150 0 1p26 bd0065 6 nuc diff straight 0.164 0 1p51 pd0426 6 prot-nuc diff straight 0.503 0 1pbl ------ 6 nuc NMR straight 0.155 0 1pbm ------ 6 nuc NMR straight 0.056 0 1q2r pr0101 6 prot-nuc diff straight 0.319 0 1q2s pr0102 6 prot-nuc diff straight 0.343 0 1qch ------ 6 nuc NMR straight 0.243 0 1qda dd0022 6 nuc diff straight 0.886 0 1s9b bd0069 6 nuc diff straight 0.194 0 1uqa ------ 6 nuc NMR straight 0.050 0 1uqb ------ 6 nuc NMR straight 0.091 0 1uqc ------ 6 nuc NMR straight 0.311 0 1uqd ------ 6 nuc NMR straight 0.027 0 1uqe ------ 6 nuc NMR straight 0.216 0 1uqf ------ 6 nuc NMR straight 0.162 0 1uqg ------ 6 nuc NMR straight 0.146 0 1x95 ------ 6 nuc NMR straight 0.369 0 206d bdf062 6 nuc diff straight 0.303 0 215d ddf053 6 nuc diff straight 0.453 0 224d ddf052 6 nuc diff straight 0.089 0 234d ddf054 6 nuc diff straight 0.277 0 235d ddf055 6 nuc diff straight 0.324 0 236d ddf056 6 nuc diff straight 0.361 0 245d ddf063 6 nuc diff straight 0.120 0 251d bdf068 6 nuc diff straight 0.048 0 254d adfb62 6 nuc diff straight 0.145 0 256d adfb72 6 nuc diff straight 0.170 0 257d adf073 6 nuc diff straight 0.445 0 258d ddf064 6 nuc diff straight 0.355 0 275d adfb63 6 nuc diff straight 0.116 0 276d ddf066 6 nuc diff straight 0.372 0 277d ddf067 6 nuc diff straight 0.776 0 278d ddf068 6 nuc diff straight 0.663 0 282d ddf069 6 nuc diff straight 0.073 0 288d ddf065 6 nuc diff straight 0.344 0 2d34 ddfb24 6 nuc diff straight 0.381 0 2da8 ------ 6 nuc NMR straight 0.855 0 2des ddf041 6 nuc diff straight 0.557 0 308d ddfb70 6 nuc diff straight 0.590 0 310d arfs26 6 nuc diff straight 0.081 0 332d ahh089 6 nuc diff straight 0.475 0 343d adfb97 6 nuc diff straight 0.778 0 366d ddf073 6 nuc diff straight 0.176 0 367d ddf074 6 nuc diff straight 0.235 0 377d arf0108 6 nuc diff straight 0.055 0 380d ddfb76 6 nuc diff straight 0.531 0 385d ddf078 6 nuc diff straight 0.305 0 386d ddf079 6 nuc diff straight 0.374 0 418d dr0001 6 nuc diff straight 0.729 0 452d dd0012 6 nuc diff straight 0.224 0 465d dd0015 6 nuc diff straight 0.234 0 482d dd0017 6 nuc diff straight 0.446 0 7ice pde047 6 prot-nuc diff straight 0.251 0 7icf pde048 6 prot-nuc diff straight 0.385 0 7icg pde049 6 prot-nuc diff straight 0.187 0 7ich pde050 6 prot-nuc diff straight 0.433 0 7ici pde051 6 prot-nuc diff straight 0.315 0 7icj pde052 6 prot-nuc diff straight 0.353 0 7ick pde053 6 prot-nuc diff straight 0.154 0 7icl pde054 6 prot-nuc diff straight 0.242 0 7icm pde055 6 prot-nuc diff straight 0.221 0 7icn pde056 6 prot-nuc diff straight 0.181 0 7ico pde057 6 prot-nuc diff straight 0.263 0 7icp pde058 6 prot-nuc diff straight 0.211 0 7icq pde059 6 prot-nuc diff straight 0.269 0 7icr pde060 6 prot-nuc diff straight 0.152 0 7ics pde061 6 prot-nuc diff straight 0.167 0 7ict pde062 6 prot-nuc diff straight 0.235 0 7icu pde063 6 prot-nuc diff straight 0.472 0 7icv pde088 6 prot-nuc diff straight 0.361 0 9ick pde0100 6 prot-nuc diff straight 0.153 0 9icl pde0101 6 prot-nuc diff straight 0.183 0 9icm pde0102 6 prot-nuc diff straight 0.183 0 9icn pde0103 6 prot-nuc diff straight 0.216 0 9ico pde0104 6 prot-nuc diff straight 0.195 0 9icp pde0105 6 prot-nuc diff straight 0.198 0 9icq pde0106 6 prot-nuc diff straight 0.222 0 9icr pde0107 6 prot-nuc diff straight 0.285 0 9ics pde0108 6 prot-nuc diff straight 0.342 0 9ict pde0109 6 prot-nuc diff straight 0.284 0 9icu pde0110 6 prot-nuc diff straight 0.212 0 9icw pde0112 6 prot-nuc diff straight 0.265 0 9icx pde0113 6 prot-nuc diff straight 0.222 0 1hu0 pd0195 7 prot-nuc diff straight 0.238 0 1lwv pd0321 7 prot-nuc diff straight 0.145 0 1lww pd0322 7 prot-nuc diff straight 0.103 0 1lwy pd0323 7 prot-nuc diff straight 0.226 0 1lyr ------ 7 prot-nuc model straight 0.297 0 1n39 pd0357 7 prot-nuc diff straight 0.288 0 1n3a pd0355 7 prot-nuc diff straight 0.200 0 1n3c pd0356 7 prot-nuc diff straight 0.214 0 1nnj pd0389 7 prot-nuc diff straight 0.259 0 1o3z ar0046 7 nuc diff straight 0.067 0 1p71 pd0430 7 prot-nuc diff straight 0.325 0 1p78 pd0431 7 prot-nuc diff straight 0.304 0 1zqa pde027 7 prot-nuc diff straight 0.120 0 1zqb pde028 7 prot-nuc diff straight 0.236 0 1zqc pde029 7 prot-nuc diff straight 0.344 0 1zqd pde030 7 prot-nuc diff straight 0.325 0 1zqf pde032 7 prot-nuc diff straight 0.197 0 1zqg pde033 7 prot-nuc diff straight 0.259 0 1zqi pde035 7 prot-nuc diff straight 0.181 0 1zqj pde036 7 prot-nuc diff straight 0.239 0 1zqk pde037 7 prot-nuc diff straight 0.060 0 1zql pde038 7 prot-nuc diff straight 0.163 0 1zqn pde040 7 prot-nuc diff straight 0.245 0 1zqo pde041 7 prot-nuc diff straight 0.261 0 1zqp pde042 7 prot-nuc diff straight 0.129 0 1zqr pde044 7 prot-nuc diff straight 0.335 0 1zqs pde045 7 prot-nuc diff straight 0.293 0 1zqt pde046 7 prot-nuc diff straight 0.256 0 2bpf pde011 7 prot-nuc diff straight 0.384 0 435d ar0010 7 nuc diff straight 0.206 0 8ica pde089 7 prot-nuc diff straight 0.224 0 8icb pde064 7 prot-nuc diff straight 0.198 0 8icc pde065 7 prot-nuc diff straight 0.161 0 8ice pde066 7 prot-nuc diff straight 0.128 0 8ich pde069 7 prot-nuc diff straight 0.068 0 8icj pde071 7 prot-nuc diff straight 0.110 0 8icm pde074 7 prot-nuc diff straight 0.128 0 8icn pde075 7 prot-nuc diff straight 0.059 0 8ico pde076 7 prot-nuc diff straight 0.145 0 8icp pde077 7 prot-nuc diff straight 0.113 0 8icq pde078 7 prot-nuc diff straight 0.164 0 8icr pde079 7 prot-nuc diff straight 0.128 0 8ics pde080 7 prot-nuc diff straight 0.069 0 8icu pde082 7 prot-nuc diff straight 0.137 0 8icv pde083 7 prot-nuc diff straight 0.096 0 8icw pde084 7 prot-nuc diff straight 0.174 0 8icy pde086 7 prot-nuc diff straight 0.172 0 8icz pde087 7 prot-nuc diff straight 0.086 0 9ica pde091 7 prot-nuc diff straight 0.105 0 9icj pde099 7 prot-nuc diff straight 0.109 0 9icy pde0114 7 prot-nuc diff straight 0.109 0 108d ------ 8 nuc NMR straight 0.381 0 118d adh047 8 nuc diff straight 0.052 0 187d adh056 8 nuc diff straight 0.057 0 189d adh058 8 nuc diff straight 0.026 0 1but ------ 8 nuc NMR straight 0.055 0 1cp8 ------ 8 nuc NMR straight 0.631 0 1d0e pd0135 8 prot-nuc diff straight 0.285 0 1d19 ------ 8 nuc NMR straight 0.109 0 1d26 adhp36 8 nuc diff straight 0.034 0 1d82 adh041 8 nuc diff straight 0.031 0 1dns adh014 8 nuc diff straight 0.008 0 1dsc ------ 8 prot-nuc NMR straight 0.749 0 1dsd ------ 8 prot-nuc NMR straight 0.200 0 1eka ------ 8 nuc NMR straight 0.218 0 1eki ------ 8 nuc NMR straight 0.962 0 1enn bd0037 8 nuc diff straight 0.186 0 1g80 ------ 8 nuc NMR straight 0.014 0 1gau ------ 8 prot-nuc NMR straight 0.169 0 1h38 ------ 8 prot-nuc diff straight 0.080 0 1huz pd0197 8 prot-nuc diff straight 0.129 0 1jtl dd0042 8 nuc diff straight 0.104 0 1k2z dd0046 8 nuc diff straight 0.071 0 1lc4 dr0007 8 nuc diff straight 0.158 0 1mwg ------ 8 nuc NMR straight 0.097 0 1mwl dr0008 8 nuc diff straight 0.359 0 1nxr ------ 8 nuc NMR straight 0.121 0 1oup pd0403 8 prot-nuc diff straight 0.514 0 1vaq dd0063 8 nuc diff straight 0.821 0 203d ------ 8 nuc NMR straight 0.506 0 209d ddh051 8 nuc diff straight 0.242 0 250d bdh071 8 nuc diff straight 0.079 0 28dn adh023 8 nuc diff straight 0.218 0 295d adh033 8 nuc diff straight 0.034 0 2d94 adh026 8 nuc diff straight 0.074 0 315d ahh077 8 nuc diff straight 0.836 0 337d adhb91 8 nuc diff straight 0.107 0 338d adhb92 8 nuc diff straight 0.051 0 339d adhb93 8 nuc diff straight 0.080 0 340d adhb94 8 nuc diff straight 0.058 0 341d adhb95 8 nuc diff straight 0.051 0 342d adhb96 8 nuc diff straight 0.082 0 345d adhb100 8 nuc diff straight 0.049 0 346d adhb101 8 nuc diff straight 0.084 0 371d adh0105 8 nuc diff straight 0.255 0 3orc pd0022 8 prot-nuc diff straight 0.108 0 472d ar0022 8 nuc diff straight 0.205 0 473d dd0016 8 nuc diff straight 0.259 0 5ana adh024 8 nuc diff straight 0.245 0 8drh ------ 8 nuc NMR straight 0.067 0 9dna adh008 8 nuc diff straight 0.129 0 1drn ------ 9 nuc NMR straight 0.302 0 1gm5 pd0267 9 prot-nuc diff straight 0.127 0 122d bdjb49 10 nuc diff straight 0.368 0 123d bdjb50 10 nuc diff straight 0.343 0 158d bdj052 10 nuc diff straight 0.394 0 169d ------ 10 nuc NMR straight 0.044 0 183d bdjb57 10 nuc diff straight 0.222 0 1aay pdt039 10 prot-nuc diff straight 0.209 0 1axp ------ 10 nuc NMR straight 0.004 0 1bd1 bdj017 10 nuc diff straight 0.210 0 1bhm pde020 10 prot-nuc diff straight 0.164 0 1cqo ------ 10 nuc NMR straight 0.395 0 1cw9 bd0021 10 nuc diff straight 0.159 0 1d02 pd0151 10 prot-nuc diff straight 0.163 0 1d61 bdjb44 10 nuc diff straight 0.418 0 1d62 bd0055 10 nuc diff straight 0.223 0 1da3 bdjb48 10 nuc diff straight 0.129 0 1di2 pr0020 10 prot-nuc diff straight 0.277 0 1ehv bd0032 10 nuc diff straight 0.048 0 1en3 bd0033 10 nuc diff straight 0.391 0 1en9 bd0035 10 nuc diff straight 0.206 0 1ene bd0036 10 nuc diff straight 0.186 0 1k4s pd0255 10 prot-nuc diff straight 0.081 0 1ku7 pd0284 10 prot-nuc diff straight 0.238 0 1nfk pdt015 10 prot-nuc diff straight 0.255 0 1rrd ------ 10 nuc NMR straight 0.126 0 1rrr ------ 10 nuc NMR straight 0.031 0 252d bdj069 10 nuc diff straight 0.070 0 274d gdjb29 10 nuc diff straight 0.034 0 2bam pd0029 10 prot-nuc diff straight 0.275 0 307d bdj081 10 nuc diff straight 0.050 0 318d adjb79 10 nuc diff straight 0.289 0 322d adjb83 10 nuc diff straight 0.615 0 325d adjb86 10 nuc diff straight 0.318 0 375d gdj059 10 nuc diff straight 0.037 0 382d adj0109 10 nuc diff straight 0.080 0 3dnb bdj008 10 nuc diff straight 0.168 0 476d bd0018 10 nuc diff straight 0.046 0 5dnb bdj019 10 nuc diff straight 0.359 0 157d arl048 12 nuc diff straight 0.187 0 1ckq pd0049 12 prot-nuc diff straight 0.216 0 1cl8 pd0054 12 prot-nuc diff straight 0.247 0 1eri pde001 12 prot-nuc diff straight 0.163 0 1gd2 pd0180 12 prot-nuc diff straight 0.650 0 1qps pd0055 12 prot-nuc diff straight 0.143 0 1qri pd0063 12 prot-nuc diff straight 0.247 0 423d bd0001 12 nuc diff straight 0.191 0 424d bd0002 12 nuc diff straight 0.181 0 425d bd0003 12 nuc diff straight 0.162 0 4bna bdlb04 12 nuc diff straight 0.103 0 1lai ------ 13 nuc NMR straight 0.101 0 1lej ------ 13 nuc NMR straight 0.191 0 1qaa ------ 20 prot-nuc model single-kink 0.000 0 0 The following structure has a goodness-of-fit value larger than 2 and is, therefore, mentioned separately. Number of structures: 9 PDB NDB bp molecule method helical s(2) r a/a2 a2 a1+a2 M type axis shape 1fja ------ 6 prot-nuc NMR straight 4.685 0 1j9n ------ 6 prot-nuc NMR straight 5.903 0 1n1k ------ 6 nuc NMR straight 2.866 0 1n35 pr0087 6 prot-nuc diff straight 5.631 0 1nzm ------ 7 nuc NMR straight 5.708 0 1kd3 ar0036 10 nuc diff straight 2.147 0 1kd4 ar0037 10 nuc diff straight 3.100 0 1kd5 ar0038 10 nuc diff straight 2.315 0 1k71 bd0056 11 nuc diff straight 3.107 0 -------------------------------------------------------------------------- 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)