HEADER RIBOSOME 31-DEC-69 5OBM TITLE Crystal structure of Gentamicin bound to the yeast 80S ribosome COMPND MOL_ID: 1; COMPND 2 MOLECULE: 25S ribosomal RNA; COMPND 3 CHAIN: 1, 5; COMPND 4 MOL_ID: 13; COMPND 5 60S ribosomal protein L11-B; COMPND 6 CHAIN: M1, m1; COMPND 7 MOL_ID: 22; COMPND 8 60S ribosomal protein L21-A; COMPND 9 CHAIN: N1, n1; COMPND 10 MOL_ID: 32; COMPND 11 60S ribosomal protein L31-A; COMPND 12 CHAIN: O1, o1; COMPND 13 MOL_ID: 42; COMPND 14 60S ribosomal protein L41-A; COMPND 15 CHAIN: Q1, q1; COMPND 16 MOL_ID: 47; COMPND 17 40S ribosomal protein S1-A; COMPND 18 CHAIN: S1, s1; COMPND 19 MOL_ID: 57; COMPND 20 40S ribosomal protein S11-A; COMPND 21 CHAIN: C1, c1; COMPND 22 MOL_ID: 67; COMPND 23 40S ribosomal protein S21-A; COMPND 24 CHAIN: D1, d1; COMPND 25 MOL_ID: 77; COMPND 26 Ubiquitin-40S ribosomal protein S31; COMPND 27 CHAIN: E1, e1; COMPND 28 MOL_ID: 83; COMPND 29 Ribosomal protein P1 alpha; COMPND 30 CHAIN: p1; COMPND 31 MOL_ID: 42; COMPND 32 60S ribosomal protein L41-A; COMPND 33 CHAIN: Q1, q1; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 3.40 ANGSTORMS DBREF 5OBM 1 1 3396 REF 83141613 NR_132207.1 3252 6647 DBREF 5OBM Q 1 25 UNP P0CX86 RL41A_YEAST 1 25 SEQRES 1 Q1 25 MET ARG ALA LYS TRP ARG LYS LYS ARG THR ARG ARG LEU SEQRES 2 Q1 25 LYS ARG LYS ARG ARG LYS VAL ARG ALA ARG SER LYS ATOM 1 N MET Q 1 -48.298 -3.571 77.363 1.00 83.54 ATOM 2 CA MET Q 1 -47.553 -4.219 78.431 1.00 83.47 ATOM 3 C MET Q 1 -47.931 -3.619 79.770 1.00 83.68 ATOM 4 O MET Q 1 -48.386 -2.469 79.830 1.00 83.79 ATOM 5 CB MET Q 1 -46.062 -4.070 78.204 1.00 83.07 ATOM 6 CG MET Q 1 -45.639 -2.623 78.095 1.00 82.92 ATOM 7 SD MET Q 1 -43.930 -2.334 78.599 1.00 82.55 ATOM 8 CE MET Q 1 -43.405 -3.995 79.037 1.00 82.51 ATOM 9 N ARG Q 2 -47.703 -4.388 80.836 1.00 77.33 ATOM 10 CA ARG Q 2 -48.166 -4.010 82.166 1.00 77.60 ATOM 11 C ARG Q 2 -47.740 -2.592 82.525 1.00 77.52 ATOM 12 O ARG Q 2 -46.588 -2.206 82.325 1.00 77.19 ATOM 13 CB ARG Q 2 -47.629 -4.995 83.198 1.00 77.62 ATOM 14 CG ARG Q 2 -47.708 -4.459 84.602 1.00 77.82 ATOM 15 CD ARG Q 2 -48.732 -5.186 85.431 1.00 78.21 ATOM 16 NE ARG Q 2 -48.182 -6.383 86.059 1.00 78.20 ATOM 17 CZ ARG Q 2 -47.736 -6.433 87.307 1.00 78.29 ATOM 18 NH1 ARG Q 2 -47.776 -5.352 88.069 1.00 78.38 ATOM 19 NH2 ARG Q 2 -47.256 -7.566 87.796 1.00 78.29 ATOM 20 N ALA Q 3 -48.686 -1.813 83.049 1.00 84.55 ATOM 21 CA ALA Q 3 -48.421 -0.408 83.341 1.00 84.52 ATOM 22 C ALA Q 3 -47.208 -0.220 84.235 1.00 84.33 ATOM 23 O ALA Q 3 -46.478 0.762 84.087 1.00 84.13 ATOM 24 CB ALA Q 3 -49.646 0.233 83.993 1.00 84.92 ATOM 25 N LYS Q 4 -46.979 -1.144 85.170 1.00 81.23 ATOM 26 CA LYS Q 4 -45.819 -1.038 86.051 1.00 81.07 ATOM 27 C LYS Q 4 -44.513 -1.282 85.295 1.00 80.64 ATOM 28 O LYS Q 4 -43.535 -0.545 85.482 1.00 80.43 ATOM 29 CB LYS Q 4 -45.953 -2.013 87.225 1.00 81.29 ATOM 30 CG LYS Q 4 -44.752 -2.002 88.152 1.00 81.15 ATOM 31 CD LYS Q 4 -45.135 -2.087 89.614 1.00 81.49 ATOM 32 CE LYS Q 4 -45.484 -3.503 89.994 1.00 81.66 ATOM 33 NZ LYS Q 4 -45.667 -3.647 91.459 1.00 81.98 ATOM 34 N TRP Q 5 -44.469 -2.312 84.443 1.00 92.54 ATOM 35 CA TRP Q 5 -43.266 -2.563 83.653 1.00 92.15 ATOM 36 C TRP Q 5 -43.092 -1.519 82.561 1.00 91.96 ATOM 37 O TRP Q 5 -41.961 -1.160 82.214 1.00 91.65 ATOM 38 CB TRP Q 5 -43.311 -3.966 83.056 1.00 92.11 ATOM 39 CG TRP Q 5 -43.636 -5.065 84.035 1.00 92.35 ATOM 40 CD1 TRP Q 5 -44.289 -6.222 83.751 1.00 92.50 ATOM 41 CD2 TRP Q 5 -43.329 -5.118 85.445 1.00 92.48 ATOM 42 NE1 TRP Q 5 -44.406 -6.997 84.879 1.00 92.72 ATOM 43 CE2 TRP Q 5 -43.826 -6.342 85.932 1.00 92.71 ATOM 44 CE3 TRP Q 5 -42.685 -4.254 86.339 1.00 92.44 ATOM 45 CZ2 TRP Q 5 -43.702 -6.724 87.269 1.00 92.90 ATOM 46 CZ3 TRP Q 5 -42.563 -4.637 87.675 1.00 92.63 ATOM 47 CH2 TRP Q 5 -43.067 -5.860 88.123 1.00 92.86 ATOM 48 N ARG Q 6 -44.195 -1.027 82.008 1.00102.50 ATOM 49 CA ARG Q 6 -44.122 0.147 81.157 1.00102.36 ATOM 50 C ARG Q 6 -43.600 1.337 81.938 1.00102.34 ATOM 51 O ARG Q 6 -42.822 2.142 81.420 1.00102.10 ATOM 52 CB ARG Q 6 -45.501 0.440 80.589 1.00102.64 ATOM 53 CG ARG Q 6 -45.672 1.840 80.087 1.00102.63 ATOM 54 CD ARG Q 6 -45.487 1.938 78.588 1.00102.43 ATOM 55 NE ARG Q 6 -46.442 2.895 78.030 1.00102.62 ATOM 56 CZ ARG Q 6 -46.302 4.219 78.063 1.00102.61 ATOM 57 NH1 ARG Q 6 -45.227 4.779 78.628 1.00102.42 ATOM 58 NH2 ARG Q 6 -47.244 4.991 77.528 1.00102.82 ATOM 59 N LYS Q 7 -44.026 1.467 83.192 1.00 90.29 ATOM 60 CA LYS Q 7 -43.499 2.521 84.045 1.00 90.28 ATOM 61 C LYS Q 7 -42.013 2.330 84.276 1.00 89.97 ATOM 62 O LYS Q 7 -41.249 3.295 84.224 1.00 89.79 ATOM 63 CB LYS Q 7 -44.248 2.551 85.377 1.00 90.66 ATOM 64 CG LYS Q 7 -43.802 3.631 86.334 1.00 90.72 ATOM 65 CD LYS Q 7 -44.598 3.559 87.638 1.00 91.11 ATOM 66 CE LYS Q 7 -44.260 4.717 88.586 1.00 91.21 ATOM 67 NZ LYS Q 7 -44.930 4.667 89.932 1.00 91.61 ATOM 68 N LYS Q 8 -41.580 1.087 84.513 1.00 75.39 ATOM 69 CA LYS Q 8 -40.158 0.836 84.738 1.00 75.09 ATOM 70 C LYS Q 8 -39.349 1.005 83.459 1.00 74.73 ATOM 71 O LYS Q 8 -38.198 1.441 83.515 1.00 74.49 ATOM 72 CB LYS Q 8 -39.943 -0.562 85.318 1.00 75.14 ATOM 73 CG LYS Q 8 -38.694 -0.702 86.183 1.00 75.00 ATOM 74 CD LYS Q 8 -38.031 -2.070 86.002 1.00 74.84 ATOM 75 CE LYS Q 8 -38.787 -3.201 86.690 1.00 75.12 ATOM 76 NZ LYS Q 8 -38.459 -3.328 88.138 1.00 75.29 ATOM 77 N ARG Q 9 -39.923 0.664 82.305 1.00 90.86 ATOM 78 CA ARG Q 9 -39.257 0.932 81.032 1.00 90.56 ATOM 79 C ARG Q 9 -38.980 2.422 80.865 1.00 90.48 ATOM 80 O ARG Q 9 -37.848 2.833 80.577 1.00 90.21 ATOM 81 CB ARG Q 9 -40.120 0.404 79.885 1.00 90.62 ATOM 82 CG ARG Q 9 -39.817 0.980 78.517 1.00 90.40 ATOM 83 CD ARG Q 9 -40.963 0.684 77.547 1.00 90.56 ATOM 84 NE ARG Q 9 -40.702 -0.375 76.558 1.00 90.41 ATOM 85 CZ ARG Q 9 -40.610 -1.678 76.834 1.00 90.42 ATOM 86 NH1 ARG Q 9 -40.717 -2.109 78.084 1.00 90.58 ATOM 87 NH2 ARG Q 9 -40.393 -2.563 75.864 1.00 90.30 ATOM 88 N THR Q 10 -40.009 3.248 81.061 1.00 97.29 ATOM 89 CA THR Q 10 -39.856 4.692 80.935 1.00 97.27 ATOM 90 C THR Q 10 -38.801 5.237 81.892 1.00 97.17 ATOM 91 O THR Q 10 -38.103 6.190 81.547 1.00 97.00 ATOM 92 CB THR Q 10 -41.217 5.383 81.149 1.00 97.63 ATOM 93 OG1 THR Q 10 -42.017 4.634 82.080 1.00 97.90 ATOM 94 CG2 THR Q 10 -41.999 5.521 79.821 1.00 97.66 ATOM 95 N ARG Q 11 -38.646 4.641 83.079 1.00 86.04 ATOM 96 CA ARG Q 11 -37.644 5.109 84.041 1.00 85.97 ATOM 97 C ARG Q 11 -36.238 4.669 83.658 1.00 85.60 ATOM 98 O ARG Q 11 -35.296 5.464 83.722 1.00 85.43 ATOM 99 CB ARG Q 11 -37.967 4.601 85.444 1.00 86.23 ATOM 100 CG ARG Q 11 -38.734 5.577 86.280 1.00 86.55 ATOM 101 CD ARG Q 11 -39.527 4.856 87.359 1.00 86.88 ATOM 102 NE ARG Q 11 -40.184 5.789 88.280 1.00 87.21 ATOM 103 CZ ARG Q 11 -40.968 5.427 89.296 1.00 87.55 ATOM 104 NH1 ARG Q 11 -41.212 4.141 89.526 1.00 87.61 ATOM 105 NH2 ARG Q 11 -41.510 6.352 90.083 1.00 87.84 ATOM 106 N ARG Q 12 -36.078 3.388 83.313 1.00 76.61 ATOM 107 CA ARG Q 12 -34.817 2.898 82.774 1.00 76.27 ATOM 108 C ARG Q 12 -34.346 3.788 81.643 1.00 76.03 ATOM 109 O ARG Q 12 -33.193 4.225 81.614 1.00 75.80 ATOM 110 CB ARG Q 12 -34.976 1.471 82.252 1.00 76.21 ATOM 111 CG ARG Q 12 -35.049 0.363 83.286 1.00 76.38 ATOM 112 CD ARG Q 12 -35.246 -0.997 82.599 1.00 76.32 ATOM 113 NE ARG Q 12 -35.409 -2.096 83.543 1.00 76.50 ATOM 114 CZ ARG Q 12 -35.845 -3.301 83.205 1.00 76.57 ATOM 115 NH1 ARG Q 12 -36.164 -3.562 81.947 1.00 76.47 ATOM 116 NH2 ARG Q 12 -35.970 -4.247 84.120 1.00 76.74 ATOM 117 N LEU Q 13 -35.238 4.063 80.698 1.00 77.68 ATOM 118 CA LEU Q 13 -34.858 4.846 79.533 1.00 77.47 ATOM 119 C LEU Q 13 -34.486 6.271 79.920 1.00 77.48 ATOM 120 O LEU Q 13 -33.570 6.855 79.338 1.00 77.24 ATOM 121 CB LEU Q 13 -35.999 4.821 78.516 1.00 77.60 ATOM 122 CG LEU Q 13 -35.887 5.472 77.132 1.00 77.45 ATOM 123 CD1 LEU Q 13 -36.402 6.890 77.192 1.00 77.61 ATOM 124 CD2 LEU Q 13 -34.454 5.411 76.560 1.00 77.10 ATOM 125 N LYS Q 14 -35.165 6.842 80.911 1.00 84.93 ATOM 126 CA LYS Q 14 -34.910 8.234 81.267 1.00 84.98 ATOM 127 C LYS Q 14 -33.693 8.407 82.167 1.00 84.85 ATOM 128 O LYS Q 14 -33.132 9.508 82.226 1.00 84.79 ATOM 129 CB LYS Q 14 -36.144 8.842 81.940 1.00 85.35 ATOM 130 CG LYS Q 14 -36.179 10.366 81.933 1.00 85.44 ATOM 131 CD LYS Q 14 -37.342 10.877 82.751 1.00 85.83 ATOM 132 CE LYS Q 14 -38.584 10.070 82.462 1.00 86.01 ATOM 133 NZ LYS Q 14 -39.237 9.612 83.720 1.00 86.30 ATOM 134 N ARG Q 15 -33.277 7.358 82.878 1.00 98.51 ATOM 135 CA ARG Q 15 -31.984 7.403 83.547 1.00 98.35 ATOM 136 C ARG Q 15 -30.843 7.274 82.550 1.00 97.99 ATOM 137 O ARG Q 15 -29.724 7.723 82.832 1.00 97.82 ATOM 138 CB ARG Q 15 -31.901 6.303 84.598 1.00 98.45 ATOM 139 CG ARG Q 15 -30.833 6.533 85.656 1.00 98.42 ATOM 140 CD ARG Q 15 -30.917 5.444 86.696 1.00 98.57 ATOM 141 NE ARG Q 15 -31.465 4.241 86.081 1.00 98.55 ATOM 142 CZ ARG Q 15 -31.888 3.171 86.747 1.00 98.72 ATOM 143 NH1 ARG Q 15 -31.826 3.139 88.079 1.00 98.93 ATOM 144 NH2 ARG Q 15 -32.377 2.132 86.072 1.00 98.69 ATOM 145 N LYS Q 16 -31.116 6.676 81.387 1.00 96.28 ATOM 146 CA LYS Q 16 -30.169 6.635 80.281 1.00 95.96 ATOM 147 C LYS Q 16 -30.030 7.988 79.591 1.00 95.90 ATOM 148 O LYS Q 16 -28.991 8.260 78.982 1.00 95.64 ATOM 149 CB LYS Q 16 -30.625 5.560 79.291 1.00 95.90 ATOM 150 CG LYS Q 16 -29.757 5.346 78.068 1.00 95.59 ATOM 151 CD LYS Q 16 -30.462 4.396 77.085 1.00 95.61 ATOM 152 CE LYS Q 16 -29.554 3.997 75.920 1.00 95.32 ATOM 153 NZ LYS Q 16 -28.261 3.398 76.392 1.00 95.11 ATOM 154 N ARG Q 17 -31.039 8.850 79.678 1.00 80.56 ATOM 155 CA ARG Q 17 -30.936 10.131 78.994 1.00 80.52 ATOM 156 C ARG Q 17 -30.063 11.101 79.768 1.00 80.49 ATOM 157 O ARG Q 17 -29.340 11.892 79.160 1.00 80.32 ATOM 158 CB ARG Q 17 -32.321 10.735 78.754 1.00 80.80 ATOM 159 CG ARG Q 17 -33.286 9.807 78.017 1.00 80.87 ATOM 160 CD ARG Q 17 -34.168 10.547 77.021 1.00 80.99 ATOM 161 NE ARG Q 17 -35.571 10.145 77.113 1.00 81.27 ATOM 162 CZ ARG Q 17 -36.387 10.020 76.069 1.00 81.35 ATOM 163 NH1 ARG Q 17 -35.945 10.236 74.834 1.00 81.15 ATOM 164 NH2 ARG Q 17 -37.649 9.658 76.259 1.00 81.62 ATOM 165 N ARG Q 18 -30.123 11.071 81.103 1.00103.02 ATOM 166 CA ARG Q 18 -29.234 11.926 81.888 1.00103.01 ATOM 167 C ARG Q 18 -27.778 11.559 81.639 1.00102.68 ATOM 168 O ARG Q 18 -26.924 12.443 81.492 1.00102.56 ATOM 169 CB ARG Q 18 -29.557 11.824 83.384 1.00103.27 ATOM 170 CG ARG Q 18 -31.052 11.834 83.719 1.00103.61 ATOM 171 CD ARG Q 18 -31.327 11.887 85.236 1.00103.89 ATOM 172 NE ARG Q 18 -32.287 10.863 85.677 1.00104.09 ATOM 173 CZ ARG Q 18 -32.022 9.919 86.587 1.00104.13 ATOM 174 NH1 ARG Q 18 -30.826 9.872 87.177 1.00103.99 ATOM 175 NH2 ARG Q 18 -32.953 9.023 86.921 1.00104.32 ATOM 176 N LYS Q 19 -27.483 10.252 81.578 1.00 94.60 ATOM 177 CA LYS Q 19 -26.146 9.729 81.313 1.00 94.29 ATOM 178 C LYS Q 19 -25.619 10.328 80.026 1.00 94.07 ATOM 179 O LYS Q 19 -24.663 11.106 80.050 1.00 93.95 ATOM 180 CB LYS Q 19 -26.157 8.197 81.216 1.00 94.22 ATOM 181 CG LYS Q 19 -25.293 7.464 82.267 1.00 94.18 ATOM 182 CD LYS Q 19 -26.094 7.103 83.543 1.00 94.49 ATOM 183 CE LYS Q 19 -25.182 6.609 84.696 1.00 94.49 ATOM 184 NZ LYS Q 19 -25.926 5.918 85.812 1.00 94.78 ATOM 185 N VAL Q 20 -26.263 9.981 78.910 1.00 70.69 ATOM 186 CA VAL Q 20 -25.888 10.491 77.594 1.00 70.50 ATOM 187 C VAL Q 20 -25.852 12.011 77.565 1.00 70.57 ATOM 188 O VAL Q 20 -25.050 12.614 76.845 1.00 70.40 ATOM 189 CB VAL Q 20 -26.860 9.941 76.538 1.00 70.53 ATOM 190 CG1 VAL Q 20 -26.454 10.398 75.149 1.00 70.36 ATOM 191 CG2 VAL Q 20 -26.925 8.432 76.626 1.00 70.49 ATOM 192 N ARG Q 21 -26.720 12.663 78.322 1.00 83.20 ATOM 193 CA ARG Q 21 -26.669 14.118 78.347 1.00 83.30 ATOM 194 C ARG Q 21 -25.581 14.637 79.283 1.00 83.24 ATOM 195 O ARG Q 21 -24.969 15.674 78.993 1.00 83.18 ATOM 196 CB ARG Q 21 -28.030 14.679 78.732 1.00 83.63 ATOM 197 CG ARG Q 21 -28.332 15.996 78.085 1.00 83.72 ATOM 198 CD ARG Q 21 -29.806 16.139 77.945 1.00 84.00 ATOM 199 NE ARG Q 21 -30.207 17.534 77.904 1.00 84.20 ATOM 200 CZ ARG Q 21 -30.510 18.232 78.989 1.00 84.44 ATOM 201 NH1 ARG Q 21 -30.887 19.502 78.894 1.00 84.64 ATOM 202 NH2 ARG Q 21 -30.431 17.647 80.175 1.00 84.52 ATOM 203 N ALA Q 22 -25.337 13.954 80.409 1.00 82.20 ATOM 204 CA ALA Q 22 -24.216 14.323 81.272 1.00 82.14 ATOM 205 C ALA Q 22 -22.908 14.387 80.486 1.00 81.83 ATOM 206 O ALA Q 22 -22.121 15.328 80.644 1.00 81.78 ATOM 207 CB ALA Q 22 -24.094 13.336 82.434 1.00 82.22 ATOM 208 N ARG Q 23 -22.678 13.417 79.602 1.00 84.64 ATOM 209 CA ARG Q 23 -21.478 13.429 78.778 1.00 84.34 ATOM 210 C ARG Q 23 -21.359 14.686 77.928 1.00 84.32 ATOM 211 O ARG Q 23 -20.289 14.942 77.368 1.00 84.11 ATOM 212 CB ARG Q 23 -21.461 12.211 77.863 1.00 84.16 ATOM 213 CG ARG Q 23 -21.670 10.884 78.561 1.00 84.21 ATOM 214 CD ARG Q 23 -21.800 9.743 77.537 1.00 84.05 ATOM 215 NE ARG Q 23 -20.510 9.313 76.990 1.00 83.77 ATOM 216 CZ ARG Q 23 -19.930 9.849 75.918 1.00 83.59 ATOM 217 NH1 ARG Q 23 -18.752 9.399 75.493 1.00 83.35 ATOM 218 NH2 ARG Q 23 -20.530 10.841 75.271 1.00 83.68 ATOM 219 N SER Q 24 -22.420 15.465 77.806 1.00 88.39 ATOM 220 CA SER Q 24 -22.384 16.655 76.980 1.00 88.39 ATOM 221 C SER Q 24 -21.979 17.910 77.745 1.00 88.51 ATOM 222 O SER Q 24 -21.733 18.944 77.112 1.00 88.50 ATOM 223 CB SER Q 24 -23.755 16.861 76.330 1.00 88.57 ATOM 224 OG SER Q 24 -23.810 18.083 75.622 1.00 88.63 ATOM 225 N LYS Q 25 -21.881 17.847 79.076 1.00104.02 ATOM 226 CA LYS Q 25 -21.736 19.063 79.904 1.00104.21 ATOM 227 C LYS Q 25 -20.430 19.813 79.690 1.00104.05 ATOM 228 O LYS Q 25 -20.290 20.942 80.163 1.00104.20 ATOM 229 CB LYS Q 25 -21.866 18.730 81.394 1.00104.39 ATOM 230 CG LYS Q 25 -23.294 18.780 81.930 1.00104.71 ATOM 231 CD LYS Q 25 -23.356 18.531 83.445 1.00104.91 ATOM 232 CE LYS Q 25 -22.535 17.305 83.869 1.00104.72 ATOM 233 NZ LYS Q 25 -22.892 16.818 85.237 1.00104.96 ATOM 234 MG MG Q 101 -34.078 -1.787 86.741 1.00 83.22 TER