IMB Jena Image Library of Biological Macromolecules (Last update: November 15, 2004) ----------------------------------------------------------------- Comprehensive Bending Classification of Nucleic Acid Double Helix Structures Slight bending ( 0 ° < M <= 10 °) Classification II (double kink: M = max(a1, a2)) (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: 226 PDB NDB bp molecule method helical s(2) r a/a2 a2 a1+a2 M type axis shape 2hdc ------ 17 prot-nuc NMR single-kink*0.070 2 2 1by4 pd0071 15 prot-nuc diff circular 0.205 424 3 1osl ------ 18 prot-nuc NMR single-kink 0.012 3 3 1cgc bdj039 10 nuc diff circular 0.067 336 4 1d60 bdjb43 10 nuc diff circular 0.039 340 4 1lpq pd0313 22 prot-nuc diff double-kink 0.041 2 4 6 4 1lrr pd0315 12 prot-nuc diff circular 0.212 294 4 1mse ------ 11 prot-nuc NMR circular 0.089 322 4 1pyi pdt017 14 prot-nuc diff circular 0.360 277 4 474d gdjb58 10 nuc diff single-kink 0.029 4 4 109d gdl033 12 nuc diff circular 0.073 263 5 121d gdl014 12 nuc diff circular 0.121 261 5 167d bdj055 10 nuc diff circular 0.068 216 5 196d bdj060 10 nuc diff single-kink 0.102 5 5 1afz ------ 11 nuc NMR single-kink 0.116 5 5 1d44 gdl011 12 nuc diff circular 0.059 222 5 1dk9 ------ 9 nuc NMR single-kink 0.051 5 5 1g14 ------ 12 nuc NMR circular 0.049 268 5 1hq7 bd0047 12 nuc diff single-kink 0.094 5 5 1imh pd0214 13 prot-nuc diff single-kink 0.169 5 5 1lo1 ------ 13 prot-nuc NMR single-kink*0.086 5 5 1qrh pd0062 12 prot-nuc diff circular 0.223 222 5 285d bdlb76 12 nuc diff circular 0.142 243 5 296d gdl028 12 nuc diff circular 0.070 219 5 445d dd0006 12 nuc diff circular 0.060 223 5 463d bd0014 10 nuc diff circular 0.052 245 5 468d ar0016 12 nuc diff single-kink 0.047 5 5 477d bd0019 10 nuc diff circular 0.051 227 5 1agh ------ 11 nuc NMR circular 0.025 187 6 1bc7 pd0027 11 prot-nuc diff circular 0.159 188 6 1bjd ------ 12 nuc NMR circular 0.024 184 6 1cvy dd0021 10 nuc diff circular 0.136 188 6 1d43 gdl010 12 nuc diff circular 0.067 213 6 1dn9 bdl007 12 nuc diff single-kink 0.085 6 6 1dvl dd0024 10 nuc diff circular 0.126 191 6 1fkz ------ 11 nuc NMR circular 0.021 179 6 1fq2 bd0041 12 nuc diff circular 0.079 181 6 1ikk bd0051 10 nuc diff circular 0.097 197 6 1jgr bd0054 12 nuc diff circular 0.071 183 6 1jk1 pd0230 10 prot-nuc diff circular 0.137 200 6 1odh ------ 13 prot-nuc diff circular 0.153 213 6 1pyj ------ 11 nuc NMR circular 0.071 178 6 1rvi ------ 12 nuc NMR circular 0.107 199 6 265d bdlb72 12 nuc diff circular 0.042 204 6 269d gdlb43 12 nuc diff circular 0.041 207 6 286d bdjb77 10 nuc diff circular 0.091 192 6 2ezf ------ 12 prot-nuc NMR single-kink 0.072 6 6 328d gdl053 12 nuc diff circular 0.059 177 6 355d bdl084 12 nuc diff circular 0.082 177 6 3bna bdlb03 12 nuc diff circular 0.098 189 6 469d ar0015 12 nuc diff single-kink 0.043 6 6 470d ar0017 12 nuc diff single-kink 0.097 6 6 101d gdlb31 12 nuc diff single-kink 0.061 7 7 1a1k pdt058 10 prot-nuc diff circular 0.083 164 7 1a36 pde0141 22 prot-nuc diff double-kink 0.096 5 7 12 7 1cs2 ------ 12 nuc NMR circular 0.110 153 7 1d65 bdl038 12 nuc diff circular 0.057 172 7 1d68 ------ 10 nuc NMR circular 0.140 173 7 1dou bd0029 12 nuc diff circular 0.071 162 7 1ej9 pd0125 22 prot-nuc diff double-kink 0.067 7 6 13 7 1fiu pd0177 10 prot-nuc diff circular 0.326 151 7 1fky ------ 11 nuc NMR circular 0.021 151 7 1fos pdt014 19 prot-nuc diff single-kink 0.130 7 7 1g2d pd0186 15 prot-nuc diff circular 0.161 149 7 1g2f pd0187 15 prot-nuc diff circular 0.150 154 7 1g3x dd0037 12 prot-nuc diff circular 0.182 166 7 1ilc bd0052 12 nuc diff circular 0.127 152 7 1j8l bd0053 12 nuc diff circular 0.073 153 7 1jnm pd0241 20 prot-nuc diff single-kink 0.203 7 7 1juw ------ 22 prot-nuc model double-kink 0.096 5 7 12 7 1ksy pd0283 21 prot-nuc diff double-kink 0.151 7 7 14 7 1mnn pd0341 13 prot-nuc diff single-kink 0.182 7 7 1naj ------ 12 nuc NMR circular 0.019 163 7 1nk0 pd0376 11 prot-nuc diff single-kink 0.059 7 7 1qms ------ 12 nuc NMR single-kink 0.018 7 7 263d gdl039 12 nuc diff circular 0.068 155 7 266d bdlb73 12 nuc diff circular 0.042 174 7 298d gdl044 12 nuc diff circular 0.150 174 7 2d25 bdjb27 10 nuc diff circular 0.346 150 7 2dau ------ 12 nuc NMR circular 0.186 169 7 408d bdd003 10 nuc diff single-kink 0.188 7 7 428d bd0005 12 nuc diff circular 0.074 166 7 447d dd0007 12 nuc diff circular 0.073 151 7 457d bd0010 12 nuc diff circular 0.054 162 7 102d gdl032 12 nuc diff single-kink 0.053 8 8 1a1g pdt056 10 prot-nuc diff single-kink 0.111 8 8 1a1h pdt057 10 prot-nuc diff circular 0.182 147 8 1am9 pdt062 38 prot-nuc diff circular 0.626 141 8 1bc8 pd0020 9 prot-nuc diff circular 0.094 131 8 1bw7 ------ 12 nuc NMR single-kink 0.214 8 8 1cvx dd0020 10 nuc diff single-kink 0.150 8 8 1d20 ------ 10 nuc NMR single-kink 0.098 8 8 1d23 bdj025 10 nuc diff circular 0.296 138 8 1d27 bdlb26 12 nuc diff circular 0.036 141 8 1d57 bdj037 10 nuc diff single-kink 0.197 8 8 1d63 gdl016 12 nuc diff circular 0.100 136 8 1d64 gdl015 12 nuc diff circular 0.073 129 8 1d77 bdlb40 12 nuc diff circular 0.140 140 8 1d86 gdl018 12 nuc diff circular 0.080 137 8 1dl4 ------ 11 nuc NMR circular 0.189 139 8 1edr bd0031 12 nuc diff circular 0.050 132 8 1eel dd0025 12 nuc diff single-kink 0.107 8 8 1efs ------ 13 nuc NMR double-kink 0.042 8 4 12 8 1ftd dd0036 12 nuc diff circular 0.073 128 8 1fzx ------ 12 nuc NMR circular 0.020 140 8 1g3v bd0042 8 nuc diff circular 0.090 128 8 1gip ------ 12 nuc NMR circular 0.139 131 8 1jgg pdt031 10 prot-nuc diff circular 0.276 131 8 1jk2 pd0231 10 prot-nuc diff single-kink 0.110 8 8 1k4t pd0256 10 prot-nuc diff circular 0.041 128 8 1kkw ------ 10 nuc NMR circular 0.232 142 8 1lex gdl037 12 nuc diff circular 0.094 129 8 1nk8 pd0381 11 prot-nuc diff circular 0.115 143 8 1prp gdl023 12 nuc diff circular 0.073 131 8 1qc1 bd0015 10 nuc diff circular 0.058 133 8 1qv4 dd0059 12 nuc diff circular 0.066 132 8 1qv8 dd0060 12 nuc diff single-kink 0.067 8 8 1vzk ------ 12 nuc diff circular 0.080 132 8 249d bdl070 11 nuc diff circular 0.168 147 8 259d arh074 8 nuc diff circular 0.016 135 8 264d gdl026 12 nuc diff circular 0.075 134 8 267d gdlb41 12 nuc diff circular 0.087 133 8 270d bdlb74 12 nuc diff circular 0.046 147 8 2bdp pde0131 9 prot-nuc diff circular 0.064 133 8 2ezd ------ 12 prot-nuc NMR circular 0.038 128 8 2eze ------ 12 prot-nuc NMR circular 0.048 137 8 363d adls105 12 nuc diff circular 0.183 134 8 407d bdd002 10 nuc diff circular 0.171 134 8 432d dd0002 8 nuc diff circular 0.116 140 8 444d dd0005 12 nuc diff single-kink 0.044 8 8 471d ar0018 12 nuc diff single-kink 0.121 8 8 113d bdl009 12 nuc diff circular 0.032 125 9 124d ------ 8 nuc NMR circular 0.043 119 9 128d gdlb19 12 nuc diff single-kink 0.097 9 9 129d gdl021 12 nuc diff single-kink 0.097 9 9 166d gdl027 12 nuc diff single-kink 0.060 9 9 1a31 pde0142 22 prot-nuc diff double-kink 0.096 9 8 17 9 1an2 pdt023 22 prot-nuc diff double-kink 0.332 9 8 17 9 1bdn bdl015 12 nuc diff circular 0.108 127 9 1d30 gdl008 12 nuc diff single-kink 0.056 9 9 1d49 bdj031 10 nuc diff circular 0.188 127 9 1d56 bdj036 10 nuc diff single-kink 0.191 9 9 1f5t pd0170 41 prot-nuc diff double-kink 1.251 7 9 16 9 1fyl pd0183 12 prot-nuc diff circular 0.021 114 9 1g75 bd0043 12 nuc diff circular 0.065 112 9 1g8n bd0044 12 nuc diff circular 0.063 118 9 1gat ------ 8 prot-nuc NMR circular 0.102 117 9 1jj8 pd0229 12 prot-nuc diff circular 0.141 117 9 1jkq pd0236 12 prot-nuc diff circular 0.258 116 9 1kb2 pd0268 18 prot-nuc diff double-kink 0.252 9 7 16 9 1l3t pd0301 10 prot-nuc diff circular 0.209 114 9 1l3u pd0302 11 prot-nuc diff single-kink 0.166 9 9 1lat pdt030 18 prot-nuc diff double-kink 0.289 9 7 16 9 1le5 pd0307 11 prot-nuc diff circular 0.081 120 9 1ley gdl038 12 nuc diff circular 0.099 116 9 1m6f dd0052 12 nuc diff circular 0.084 115 9 1mhd pd0243 13 prot-nuc diff single-kink 0.123 9 9 1mq2 pd0343 10 prot-nuc diff circular 0.160 115 9 1ndn bdl032 12 nuc diff single-kink 0.212 9 9 1njw pd0372 11 prot-nuc diff single-kink 0.101 9 9 1nlw pd0387 18 prot-nuc diff double-kink 0.153 9 6 15 9 1rxb arh064 8 nuc diff circular 0.015 126 9 1t7p pde0135 11 prot-nuc diff single-kink 0.248 9 9 1vkx pdr033 11 prot-nuc diff single-kink 0.113 9 9 1zaa pdt006 10 prot-nuc diff single-kink 0.208 9 9 202d ------ 8 nuc NMR circular 0.366 115 9 214d ------ 11 nuc NMR circular 0.149 116 9 243d adh070 8 nuc diff circular 0.050 113 9 268d gdlb42 12 nuc diff single-kink 0.067 9 9 287d bdl078 12 nuc diff circular 0.110 113 9 297d bdlb82 12 nuc diff circular 0.080 122 9 2dbe gdl009 12 nuc diff single-kink 0.061 9 9 2dnd gdl003 12 nuc diff circular 0.151 121 9 2nll pdr021 18 prot-nuc diff double-kink 0.394 9 9 18 9 302d gdl047 12 nuc diff circular 0.042 127 9 303d gdl048 12 nuc diff circular 0.038 122 9 344d adhb99 8 nuc diff circular 0.072 113 9 3hts pd0073 12 prot-nuc diff single-kink 0.080 9 9 403d bdd001 12 nuc diff circular 0.068 123 9 431d bd0006 8 nuc diff circular 0.039 113 9 449d dd0009 12 nuc diff circular 0.059 118 9 456d bd0009 12 nuc diff circular 0.056 118 9 458d bd0011 12 nuc diff circular 0.106 117 9 459d dd0014 12 nuc diff circular 0.055 125 9 7bna bdl005 12 nuc diff circular 0.074 125 9 8bna gdl006 12 nuc diff circular 0.141 122 9 119d bdl042 12 nuc diff circular 0.585 101 10 127d gdl022 12 nuc diff single-kink 0.099 10 10 130d gdlb20 12 nuc diff single-kink 0.149 10 10 170d ------ 12 nuc NMR circular 0.639 110 10 1a1l pdt061 10 prot-nuc diff circular 0.208 105 10 1apl pdt005 20 prot-nuc diff double-kink 0.193 10 9 19 10 1cf7 pd0045 15 prot-nuc diff double-kink 0.239 7 10 17 10 1d29 bdl029 12 nuc diff circular 0.065 107 10 1d46 gdl013 12 nuc diff single-kink 0.071 10 10 1d5y pd0078 20 prot-nuc diff double-kink 0.185 10 10 20 10 1d85 gdlb17 12 nuc diff single-kink 0.126 10 10 1d89 bdl047 12 nuc diff circular 0.182 108 10 1d98 bdl006 12 nuc diff circular 0.059 105 10 1dne gdl004 12 nuc diff circular 0.243 100 10 1dnh gdl002 12 nuc diff single-kink 0.108 10 10 1fym pd0184 12 prot-nuc diff circular 0.010 99 10 1g7z ------ 8 nuc NMR circular 0.126 108 10 1gxp ------ 22 prot-nuc diff circular 0.370 103 10 1hjb pd0204 25 prot-nuc diff circular 0.291 99 10 1i47 bd0049 12 nuc diff single-kink 0.080 10 10 1iu3 pd0297 9 prot-nuc diff circular 0.217 105 10 1jx4 pd0251 13 prot-nuc diff circular 0.129 108 10 1jxl pd0252 12 prot-nuc diff single-kink 0.123 10 10 1k78 pd0259 25 prot-nuc diff double-kink 0.252 10 10 20 10 1kb4 pd0269 18 prot-nuc diff double-kink 0.209 9 10 19 10 1kb6 pd0270 18 prot-nuc diff double-kink 0.227 8 10 18 10 1l5u pd0304 12 prot-nuc diff single-kink 0.127 10 10 1le9 pd0309 11 prot-nuc diff single-kink 0.171 10 10 1lp7 bd0057 12 nuc diff circular 0.058 105 10 226d ------ 10 nuc NMR single-kink 0.174 10 10 227d gdl036 12 nuc diff single-kink 0.035 10 10 246d ahh071 8 nuc diff circular 0.069 110 10 271d bdl075 12 nuc diff circular 0.053 106 10 311d gdl052 12 nuc diff single-kink 0.052 10 10 365d gdj057 10 nuc diff single-kink 0.088 10 10 448d dd0008 12 nuc diff circular 0.060 110 10 6bna gdlb05 12 nuc diff single-kink 0.063 10 10 8icf pde067 7 prot-nuc diff circular 0.099 100 10 8ict pde081 7 prot-nuc diff circular 0.092 103 10 9ice pde094 7 prot-nuc diff circular 0.104 101 10 -------------------------------------------------------------------------- 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)