HEADER TRANSFERASE 31-DEC-69 4IJD TITLE Crystal structure of methyltransferase domain of human PR TITLE 2 domain-containing protein 9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: Histone-lysine N-methyltransferase PRDM9; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.1.1.43; COMPND 5 FRAGMENT: UNP residues ; COMPND 6 ENGINEERED: YES; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 2.15 ANGSTORMS REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA B 185 REMARK 465 GLY B 186 DBREF 4IJD B 195 415 UNP Q9NQV7 PRDM9_HUMAN 195 415 MODRES 4IJD MSE B 13 MET SELENOMETHIONINE MODRES 4IJD MSE B 122 MET SELENOMETHIONINE MODRES 4IJD MSE B 184 MET SELENOMETHIONINE SEQRES 1 B 33 ALA GLY ARG GLU PRO LYS PRO GLU ILE HIS PRO CYS PRO SEQRES 2 B 33 SER CYS CYS LEU ALA PHE SER SER GLN LYS PHE LEU SER SEQRES 3 B 33 GLN HIS VAL GLU ARG ASN HIS ATOM 1 N ARG B 381 14.226 -4.858 19.066 1.00 80.11 ATOM 2 CA ARG B 381 14.942 -3.893 18.220 1.00 81.90 ATOM 3 C ARG B 381 14.797 -2.432 18.706 1.00 82.47 ATOM 4 O ARG B 381 13.750 -1.804 18.534 1.00 83.52 ATOM 5 CB ARG B 381 14.480 -4.014 16.762 1.00 82.67 ATOM 6 N GLU B 382 15.857 -1.920 19.334 1.00 80.80 ATOM 7 CA GLU B 382 15.996 -0.489 19.645 1.00 79.54 ATOM 8 C GLU B 382 17.381 -0.026 19.143 1.00 78.67 ATOM 9 O GLU B 382 18.261 -0.851 18.917 1.00 75.19 ATOM 10 CB GLU B 382 15.843 -0.249 21.164 1.00 76.14 ATOM 11 CG GLU B 382 14.438 -0.507 21.729 1.00 75.90 ATOM 12 CD GLU B 382 13.416 0.582 21.370 1.00 78.99 ATOM 13 OE1 GLU B 382 13.698 1.781 21.600 1.00 76.75 ATOM 14 OE2 GLU B 382 12.317 0.240 20.866 1.00 80.64 ATOM 15 N PRO B 383 17.579 1.292 18.962 1.00 80.43 ATOM 16 CA PRO B 383 18.865 1.753 18.397 1.00 81.93 ATOM 17 C PRO B 383 20.089 1.567 19.343 1.00 78.56 ATOM 18 O PRO B 383 19.933 1.566 20.573 1.00 75.91 ATOM 19 CB PRO B 383 18.612 3.246 18.087 1.00 84.34 ATOM 20 CG PRO B 383 17.213 3.550 18.539 1.00 84.40 ATOM 21 CD PRO B 383 16.722 2.411 19.378 1.00 81.90 ATOM 22 N LYS B 384 21.287 1.415 18.760 1.00 77.96 ATOM 23 CA LYS B 384 22.464 0.922 19.505 1.00 74.31 ATOM 24 C LYS B 384 23.379 2.060 19.975 1.00 73.31 ATOM 25 O LYS B 384 23.818 2.889 19.162 1.00 69.23 ATOM 26 CB LYS B 384 23.272 -0.073 18.662 1.00 74.41 ATOM 27 N PRO B 385 23.673 2.098 21.296 1.00 70.14 ATOM 28 CA PRO B 385 24.649 3.047 21.842 1.00 70.25 ATOM 29 C PRO B 385 25.973 3.012 21.061 1.00 70.56 ATOM 30 O PRO B 385 26.394 1.946 20.636 1.00 69.33 ATOM 31 CB PRO B 385 24.870 2.543 23.276 1.00 67.97 ATOM 32 CG PRO B 385 23.633 1.777 23.618 1.00 69.26 ATOM 33 CD PRO B 385 23.087 1.228 22.335 1.00 68.30 ATOM 34 N GLU B 386 26.600 4.172 20.850 1.00 72.88 ATOM 35 CA GLU B 386 27.929 4.235 20.220 1.00 71.55 ATOM 36 C GLU B 386 29.018 4.245 21.305 1.00 70.04 ATOM 37 O GLU B 386 28.737 4.484 22.477 1.00 69.37 ATOM 38 CB GLU B 386 28.041 5.468 19.318 1.00 72.40 ATOM 39 N ILE B 387 30.250 3.928 20.918 1.00 68.49 ATOM 40 CA ILE B 387 31.381 3.982 21.835 1.00 64.81 ATOM 41 C ILE B 387 32.532 4.679 21.133 1.00 63.81 ATOM 42 O ILE B 387 33.086 4.162 20.163 1.00 69.54 ATOM 43 CB ILE B 387 31.837 2.577 22.288 1.00 65.87 ATOM 44 CG1 ILE B 387 30.644 1.750 22.783 1.00 65.56 ATOM 45 CG2 ILE B 387 32.882 2.675 23.405 1.00 62.84 ATOM 46 CD1 ILE B 387 31.040 0.411 23.376 1.00 63.92 ATOM 47 N HIS B 388 32.894 5.849 21.627 1.00 58.83 ATOM 48 CA HIS B 388 33.952 6.632 21.028 1.00 59.10 ATOM 49 C HIS B 388 35.094 6.786 22.019 1.00 57.74 ATOM 50 O HIS B 388 35.061 7.685 22.857 1.00 55.76 ATOM 51 CB HIS B 388 33.390 7.995 20.611 1.00 60.51 ATOM 52 CG HIS B 388 32.241 7.910 19.605 1.00 61.51 ATOM 53 ND1 HIS B 388 32.396 8.206 18.302 1.00 64.50 ATOM 54 CD2 HIS B 388 30.894 7.558 19.767 1.00 60.88 ATOM 55 CE1 HIS B 388 31.219 8.047 17.656 1.00 65.19 ATOM 56 NE2 HIS B 388 30.304 7.647 18.548 1.00 63.87 ATOM 57 N PRO B 389 36.120 5.899 21.953 1.00 57.38 ATOM 58 CA PRO B 389 37.188 6.008 22.951 1.00 56.61 ATOM 59 C PRO B 389 38.195 7.075 22.600 1.00 56.16 ATOM 60 O PRO B 389 38.371 7.389 21.430 1.00 60.18 ATOM 61 CB PRO B 389 37.846 4.601 22.946 1.00 57.49 ATOM 62 CG PRO B 389 36.936 3.741 22.113 1.00 59.14 ATOM 63 CD PRO B 389 36.299 4.693 21.135 1.00 58.90 ATOM 64 N CYS B 390 38.824 7.639 23.626 1.00 54.36 ATOM 65 CA CYS B 390 39.847 8.660 23.469 1.00 56.71 ATOM 66 C CYS B 390 41.229 8.010 23.289 1.00 58.75 ATOM 67 O CYS B 390 41.650 7.222 24.121 1.00 57.01 ATOM 68 CB CYS B 390 39.859 9.582 24.689 1.00 55.71 ATOM 69 SG CYS B 390 41.268 10.692 24.749 1.00 56.01 ATOM 70 N PRO B 391 41.943 8.350 22.203 1.00 61.71 ATOM 71 CA PRO B 391 43.258 7.743 22.018 1.00 63.61 ATOM 72 C PRO B 391 44.306 8.247 23.029 1.00 65.27 ATOM 73 O PRO B 391 45.406 7.674 23.107 1.00 66.40 ATOM 74 CB PRO B 391 43.639 8.167 20.596 1.00 66.99 ATOM 75 CG PRO B 391 42.885 9.433 20.362 1.00 66.50 ATOM 76 CD PRO B 391 41.603 9.288 21.119 1.00 63.86 ATOM 77 N SER B 392 43.974 9.302 23.785 1.00 64.77 ATOM 78 CA SER B 392 44.916 9.907 24.734 1.00 67.05 ATOM 79 C SER B 392 44.755 9.443 26.194 1.00 63.96 ATOM 80 O SER B 392 45.692 9.548 26.993 1.00 65.62 ATOM 81 CB SER B 392 44.828 11.423 24.666 1.00 69.20 ATOM 82 OG SER B 392 45.324 11.894 23.425 1.00 75.67 ATOM 83 N CYS B 393 43.587 8.924 26.545 1.00 61.73 ATOM 84 CA CYS B 393 43.394 8.372 27.887 1.00 58.70 ATOM 85 C CYS B 393 42.346 7.270 27.870 1.00 56.91 ATOM 86 O CYS B 393 41.828 6.931 26.815 1.00 56.43 ATOM 87 CB CYS B 393 43.056 9.496 28.892 1.00 58.59 ATOM 88 SG CYS B 393 41.434 10.284 28.719 1.00 57.62 ATOM 89 N CYS B 394 42.054 6.691 29.031 1.00 55.15 ATOM 90 CA CYS B 394 41.206 5.497 29.086 1.00 58.13 ATOM 91 C CYS B 394 39.711 5.780 28.966 1.00 55.92 ATOM 92 O CYS B 394 38.912 4.852 29.050 1.00 57.83 ATOM 93 CB CYS B 394 41.463 4.707 30.386 1.00 59.45 ATOM 94 SG CYS B 394 43.147 4.075 30.539 1.00 64.31 ATOM 95 N LEU B 395 39.318 7.036 28.752 1.00 55.63 ATOM 96 CA LEU B 395 37.892 7.363 28.687 1.00 54.42 ATOM 97 C LEU B 395 37.254 6.991 27.351 1.00 54.44 ATOM 98 O LEU B 395 37.954 6.735 26.357 1.00 54.80 ATOM 99 CB LEU B 395 37.661 8.842 28.997 1.00 54.10 ATOM 100 CG LEU B 395 38.113 9.287 30.391 1.00 54.33 ATOM 101 CD1 LEU B 395 37.951 10.797 30.556 1.00 56.83 ATOM 102 CD2 LEU B 395 37.351 8.546 31.486 1.00 52.08 ATOM 103 N ALA B 396 35.917 6.952 27.350 1.00 53.34 ATOM 104 CA ALA B 396 35.110 6.772 26.128 1.00 54.18 ATOM 105 C ALA B 396 33.806 7.560 26.212 1.00 52.86 ATOM 106 O ALA B 396 33.362 7.924 27.295 1.00 53.00 ATOM 107 CB ALA B 396 34.818 5.302 25.899 1.00 54.20 ATOM 108 N PHE B 397 33.193 7.831 25.064 1.00 53.42 ATOM 109 CA PHE B 397 32.012 8.719 25.014 1.00 51.77 ATOM 110 C PHE B 397 30.937 8.167 24.119 1.00 51.38 ATOM 111 O PHE B 397 31.198 7.279 23.311 1.00 50.95 ATOM 112 CB PHE B 397 32.442 10.096 24.540 1.00 53.98 ATOM 113 CG PHE B 397 33.526 10.664 25.363 1.00 53.58 ATOM 114 CD1 PHE B 397 34.842 10.311 25.128 1.00 53.66 ATOM 115 CD2 PHE B 397 33.230 11.436 26.464 1.00 52.95 ATOM 116 CE1 PHE B 397 35.852 10.769 25.948 1.00 53.66 ATOM 117 CE2 PHE B 397 34.235 11.903 27.285 1.00 52.80 ATOM 118 CZ PHE B 397 35.545 11.579 27.023 1.00 52.66 ATOM 119 N SER B 398 29.727 8.715 24.254 1.00 52.33 ATOM 120 CA SER B 398 28.530 8.205 23.563 1.00 51.50 ATOM 121 C SER B 398 28.410 8.729 22.135 1.00 54.14 ATOM 122 O SER B 398 27.612 8.224 21.334 1.00 55.88 ATOM 123 CB SER B 398 27.278 8.576 24.363 1.00 51.99 ATOM 124 OG SER B 398 27.138 9.988 24.489 1.00 52.89 ATOM 125 N SER B 399 29.217 9.739 21.810 1.00 54.82 ATOM 126 CA SER B 399 29.165 10.386 20.507 1.00 55.38 ATOM 127 C SER B 399 30.506 11.028 20.167 1.00 56.30 ATOM 128 O SER B 399 31.374 11.192 21.043 1.00 55.11 ATOM 129 CB SER B 399 28.081 11.455 20.512 1.00 56.44 ATOM 130 OG SER B 399 28.418 12.505 21.405 1.00 55.15 ATOM 131 N GLN B 400 30.670 11.382 18.899 1.00 58.50 ATOM 132 CA GLN B 400 31.890 12.040 18.425 1.00 60.38 ATOM 133 C GLN B 400 31.980 13.447 18.991 1.00 61.28 ATOM 134 O GLN B 400 33.078 13.924 19.324 1.00 60.78 ATOM 135 CB GLN B 400 31.915 12.086 16.887 1.00 63.11 ATOM 136 CG GLN B 400 33.121 12.801 16.271 1.00 65.27 ATOM 137 CD GLN B 400 34.462 12.202 16.682 1.00 64.68 ATOM 138 OE1 GLN B 400 35.356 12.910 17.159 1.00 64.80 ATOM 139 NE2 GLN B 400 34.610 10.904 16.488 1.00 63.85 ATOM 140 N LYS B 401 30.819 14.116 19.071 1.00 63.15 ATOM 141 CA LYS B 401 30.698 15.437 19.696 1.00 62.76 ATOM 142 C LYS B 401 31.336 15.468 21.092 1.00 60.94 ATOM 143 O LYS B 401 32.159 16.333 21.377 1.00 62.58 ATOM 144 CB LYS B 401 29.225 15.859 19.789 1.00 63.95 ATOM 145 N PHE B 402 30.988 14.512 21.946 1.00 58.32 ATOM 146 CA PHE B 402 31.515 14.513 23.301 1.00 57.49 ATOM 147 C PHE B 402 32.999 14.155 23.339 1.00 56.54 ATOM 148 O PHE B 402 33.738 14.686 24.164 1.00 55.93 ATOM 149 CB PHE B 402 30.710 13.576 24.221 1.00 57.11 ATOM 150 CG PHE B 402 29.313 14.073 24.531 1.00 59.31 ATOM 151 CD1 PHE B 402 29.063 15.421 24.753 1.00 61.65 ATOM 152 CD2 PHE B 402 28.256 13.182 24.629 1.00 59.61 ATOM 153 CE1 PHE B 402 27.781 15.869 25.050 1.00 63.39 ATOM 154 CE2 PHE B 402 26.974 13.624 24.917 1.00 59.95 ATOM 155 CZ PHE B 402 26.737 14.964 25.132 1.00 61.31 ATOM 156 N LEU B 403 33.438 13.256 22.459 1.00 55.64 ATOM 157 CA LEU B 403 34.860 12.912 22.400 1.00 55.61 ATOM 158 C LEU B 403 35.672 14.127 21.953 1.00 57.85 ATOM 159 O LEU B 403 36.728 14.399 22.511 1.00 58.30 ATOM 160 CB LEU B 403 35.120 11.710 21.472 1.00 56.27 ATOM 161 CG LEU B 403 36.599 11.285 21.243 1.00 57.85 ATOM 162 CD1 LEU B 403 37.304 10.857 22.532 1.00 56.14 ATOM 163 CD2 LEU B 403 36.713 10.166 20.208 1.00 58.42 ATOM 164 N SER B 404 35.175 14.863 20.963 1.00 58.94 ATOM 165 CA SER B 404 35.919 16.018 20.445 1.00 61.73 ATOM 166 C SER B 404 36.029 17.108 21.498 1.00 63.18 ATOM 167 O SER B 404 37.095 17.681 21.690 1.00 63.08 ATOM 168 CB SER B 404 35.249 16.574 19.197 1.00 62.68 ATOM 169 OG SER B 404 35.383 15.665 18.134 1.00 62.53 ATOM 170 N GLN B 405 34.914 17.380 22.186 1.00 64.26 ATOM 171 CA GLN B 405 34.910 18.326 23.306 1.00 66.00 ATOM 172 C GLN B 405 35.930 17.919 24.368 1.00 64.39 ATOM 173 O GLN B 405 36.664 18.756 24.897 1.00 66.33 ATOM 174 CB GLN B 405 33.529 18.386 23.951 1.00 66.63 ATOM 175 CG GLN B 405 32.468 19.085 23.109 1.00 69.34 ATOM 176 CD GLN B 405 31.056 18.748 23.563 1.00 68.92 ATOM 177 OE1 GLN B 405 30.856 18.062 24.570 1.00 68.24 ATOM 178 NE2 GLN B 405 30.073 19.224 22.820 1.00 72.01 ATOM 179 N HIS B 406 35.967 16.635 24.682 1.00 61.85 ATOM 180 CA HIS B 406 36.924 16.123 25.661 1.00 60.52 ATOM 181 C HIS B 406 38.357 16.365 25.247 1.00 62.29 ATOM 182 O HIS B 406 39.166 16.827 26.049 1.00 63.29 ATOM 183 CB HIS B 406 36.705 14.641 25.887 1.00 57.43 ATOM 184 CG HIS B 406 37.841 13.966 26.609 1.00 56.02 ATOM 185 ND1 HIS B 406 38.047 14.113 27.924 1.00 53.84 ATOM 186 CD2 HIS B 406 38.853 13.127 26.144 1.00 55.95 ATOM 187 CE1 HIS B 406 39.125 13.415 28.286 1.00 54.38 ATOM 188 NE2 HIS B 406 39.621 12.820 27.192 1.00 55.63 ATOM 189 N VAL B 407 38.683 16.046 23.997 1.00 62.64 ATOM 190 CA VAL B 407 40.044 16.199 23.501 1.00 64.47 ATOM 191 C VAL B 407 40.491 17.667 23.479 1.00 68.34 ATOM 192 O VAL B 407 41.638 17.976 23.835 1.00 69.41 ATOM 193 CB VAL B 407 40.215 15.547 22.100 1.00 65.13 ATOM 194 CG1 VAL B 407 41.531 15.967 21.443 1.00 65.68 ATOM 195 CG2 VAL B 407 40.139 14.023 22.218 1.00 62.44 ATOM 196 N GLU B 408 39.593 18.562 23.065 1.00 70.11 ATOM 197 CA GLU B 408 39.879 20.000 23.063 1.00 73.23 ATOM 198 C GLU B 408 40.122 20.516 24.483 1.00 74.04 ATOM 199 O GLU B 408 41.031 21.310 24.708 1.00 76.46 ATOM 200 CB GLU B 408 38.732 20.785 22.411 1.00 72.61 ATOM 201 N ARG B 409 39.327 20.030 25.436 1.00 73.57 ATOM 202 CA ARG B 409 39.305 20.575 26.805 1.00 74.67 ATOM 203 C ARG B 409 40.483 20.141 27.701 1.00 74.83 ATOM 204 O ARG B 409 40.761 20.795 28.701 1.00 75.29 ATOM 205 CB ARG B 409 37.983 20.215 27.500 1.00 72.74 ATOM 206 N ASN B 410 41.162 19.048 27.376 1.00 74.87 ATOM 207 CA ASN B 410 42.311 18.643 28.197 1.00 76.42 ATOM 208 C ASN B 410 43.328 17.733 27.514 1.00 76.24 ATOM 209 O ASN B 410 43.992 16.942 28.170 1.00 75.28 ATOM 210 CB ASN B 410 41.825 18.008 29.500 1.00 77.05 ATOM 211 CG ASN B 410 40.870 16.869 29.263 1.00 75.10 ATOM 212 OD1 ASN B 410 41.230 15.876 28.644 1.00 77.59 ATOM 213 ND2 ASN B 410 39.639 17.014 29.741 1.00 73.79 ATOM 214 N HIS B 411 43.453 17.866 26.199 1.00 77.18 ATOM 215 CA HIS B 411 44.599 17.338 25.475 1.00 76.26 ATOM 216 C HIS B 411 45.033 18.399 24.502 1.00 75.67 ATOM 217 O HIS B 411 45.830 18.147 23.616 1.00 75.45 ATOM 218 CB HIS B 411 44.255 16.022 24.744 1.00 73.57 ATOM 219 CG HIS B 411 43.906 14.870 25.664 1.00 71.16 ATOM 220 ND1 HIS B 411 44.759 14.399 26.603 1.00 70.29 ATOM 221 CD2 HIS B 411 42.756 14.060 25.738 1.00 68.97 ATOM 222 CE1 HIS B 411 44.175 13.371 27.265 1.00 66.08 ATOM 223 NE2 HIS B 411 42.960 13.160 26.730 1.00 64.50 ATOM 224 ZN ZN B 502 41.380 11.681 26.855 1.00 60.94 ATOM 225 UNK UNX B 503 35.183 -0.286 22.747 1.00 30.00 ATOM 226 UNK UNX B 506 29.950 5.847 26.967 1.00 30.00 TER