HEADER TRANSFERASE 21-DEC-12 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 DBREF 4IJD A 195 415 UNP Q9NQV7 PRDM9_HUMAN 195 415 MODRES 4IJD MSE A 13 MET SELENOMETHIONINE MODRES 4IJD MSE A 122 MET SELENOMETHIONINE MODRES 4IJD MSE A 184 MET SELENOMETHIONINE SEQRES 1 A 25 PRO CYS PRO SER CYS CYS LEU ALA PHE SER SER GLN LYS SEQRES 2 A 25 PHE LEU SER GLN HIS VAL GLU ARG ASN HIS SER SER ATOM 1 N PRO A 389 18.053 -10.804 12.847 1.00 45.95 ATOM 2 CA PRO A 389 18.954 -10.876 11.699 1.00 43.19 ATOM 3 C PRO A 389 20.035 -11.919 11.869 1.00 40.50 ATOM 4 O PRO A 389 20.505 -12.139 12.964 1.00 43.08 ATOM 5 CB PRO A 389 19.570 -9.459 11.624 1.00 42.52 ATOM 6 CG PRO A 389 19.355 -8.840 12.975 1.00 46.39 ATOM 7 CD PRO A 389 18.360 -9.666 13.748 1.00 47.07 ATOM 8 N CYS A 390 20.429 -12.548 10.774 1.00 39.04 ATOM 9 CA CYS A 390 21.638 -13.404 10.765 1.00 40.54 ATOM 10 C CYS A 390 22.933 -12.573 10.792 1.00 41.07 ATOM 11 O CYS A 390 23.087 -11.633 10.014 1.00 39.77 ATOM 12 CB CYS A 390 21.639 -14.259 9.517 1.00 39.35 ATOM 13 SG CYS A 390 22.870 -15.555 9.498 1.00 39.85 ATOM 14 N PRO A 391 23.901 -12.961 11.636 1.00 45.58 ATOM 15 CA PRO A 391 25.170 -12.247 11.654 1.00 47.09 ATOM 16 C PRO A 391 26.115 -12.578 10.479 1.00 47.45 ATOM 17 O PRO A 391 27.166 -11.953 10.367 1.00 47.80 ATOM 18 CB PRO A 391 25.799 -12.738 12.951 1.00 50.66 ATOM 19 CG PRO A 391 25.331 -14.155 13.047 1.00 49.65 ATOM 20 CD PRO A 391 23.915 -14.113 12.563 1.00 47.72 ATOM 21 N SER A 392 25.781 -13.574 9.649 1.00 46.14 ATOM 22 CA SER A 392 26.739 -14.088 8.631 1.00 44.08 ATOM 23 C SER A 392 26.264 -13.950 7.195 1.00 43.07 ATOM 24 O SER A 392 26.951 -14.398 6.274 1.00 46.02 ATOM 25 CB SER A 392 27.021 -15.566 8.872 1.00 43.15 ATOM 26 OG SER A 392 27.573 -15.759 10.143 1.00 48.27 ATOM 27 N CYS A 393 25.041 -13.472 7.015 1.00 40.07 ATOM 28 CA CYS A 393 24.471 -13.280 5.685 1.00 37.73 ATOM 29 C CYS A 393 23.354 -12.280 5.834 1.00 36.48 ATOM 30 O CYS A 393 23.124 -11.762 6.928 1.00 34.78 ATOM 31 CB CYS A 393 23.965 -14.575 5.069 1.00 35.55 ATOM 32 SG CYS A 393 22.285 -15.074 5.569 1.00 36.36 ATOM 33 N CYS A 394 22.686 -11.988 4.737 1.00 34.96 ATOM 34 CA CYS A 394 21.801 -10.825 4.673 1.00 37.28 ATOM 35 C CYS A 394 20.382 -11.136 5.114 1.00 37.83 ATOM 36 O CYS A 394 19.557 -10.236 5.150 1.00 40.04 ATOM 37 CB CYS A 394 21.817 -10.217 3.256 1.00 37.01 ATOM 38 SG CYS A 394 23.475 -9.666 2.732 1.00 43.40 ATOM 39 N LEU A 395 20.107 -12.384 5.514 1.00 35.78 ATOM 40 CA LEU A 395 18.753 -12.778 5.895 1.00 35.83 ATOM 41 C LEU A 395 18.348 -12.347 7.301 1.00 35.14 ATOM 42 O LEU A 395 19.184 -12.086 8.127 1.00 35.59 ATOM 43 CB LEU A 395 18.571 -14.298 5.745 1.00 36.17 ATOM 44 CG LEU A 395 18.918 -14.885 4.369 1.00 36.56 ATOM 45 CD1 LEU A 395 18.646 -16.389 4.334 1.00 37.65 ATOM 46 CD2 LEU A 395 18.162 -14.158 3.262 1.00 36.12 ATOM 47 N ALA A 396 17.035 -12.292 7.557 1.00 35.21 ATOM 48 CA ALA A 396 16.533 -12.202 8.931 1.00 36.64 ATOM 49 C ALA A 396 15.277 -13.048 9.129 1.00 36.77 ATOM 50 O ALA A 396 14.614 -13.417 8.176 1.00 34.89 ATOM 51 CB ALA A 396 16.268 -10.761 9.304 1.00 36.15 ATOM 52 N PHE A 397 14.979 -13.361 10.390 1.00 37.67 ATOM 53 CA PHE A 397 13.972 -14.331 10.723 1.00 38.43 ATOM 54 C PHE A 397 12.985 -13.794 11.721 1.00 42.32 ATOM 55 O PHE A 397 13.235 -12.786 12.383 1.00 44.49 ATOM 56 CB PHE A 397 14.648 -15.597 11.185 1.00 40.16 ATOM 57 CG PHE A 397 15.508 -16.179 10.130 1.00 38.80 ATOM 58 CD1 PHE A 397 16.803 -15.678 9.914 1.00 36.71 ATOM 59 CD2 PHE A 397 14.978 -17.090 9.235 1.00 38.13 ATOM 60 CE1 PHE A 397 17.568 -16.147 8.866 1.00 37.03 ATOM 61 CE2 PHE A 397 15.739 -17.575 8.192 1.00 37.62 ATOM 62 CZ PHE A 397 17.032 -17.091 7.989 1.00 37.51 ATOM 63 N SER A 398 11.828 -14.430 11.782 1.00 43.84 ATOM 64 CA SER A 398 10.747 -13.926 12.618 1.00 46.35 ATOM 65 C SER A 398 10.855 -14.443 14.050 1.00 45.90 ATOM 66 O SER A 398 10.105 -14.029 14.919 1.00 49.79 ATOM 67 CB SER A 398 9.392 -14.290 12.000 1.00 46.00 ATOM 68 OG SER A 398 9.247 -15.697 11.921 1.00 48.21 ATOM 69 N SER A 399 11.774 -15.369 14.302 1.00 47.75 ATOM 70 CA SER A 399 12.013 -15.824 15.682 1.00 48.54 ATOM 71 C SER A 399 13.439 -16.311 15.881 1.00 48.64 ATOM 72 O SER A 399 14.211 -16.429 14.916 1.00 43.80 ATOM 73 CB SER A 399 11.031 -16.931 16.054 1.00 50.86 ATOM 74 OG SER A 399 11.274 -18.103 15.285 1.00 51.59 ATOM 75 N GLN A 400 13.773 -16.612 17.133 1.00 50.64 ATOM 76 CA GLN A 400 15.092 -17.123 17.481 1.00 52.65 ATOM 77 C GLN A 400 15.236 -18.540 16.968 1.00 53.86 ATOM 78 O GLN A 400 16.256 -18.878 16.386 1.00 54.50 ATOM 79 CB GLN A 400 15.295 -17.091 18.995 1.00 56.90 ATOM 80 CG GLN A 400 15.195 -15.692 19.587 1.00 57.71 ATOM 81 N LYS A 401 14.207 -19.365 17.193 1.00 56.11 ATOM 82 CA LYS A 401 14.139 -20.726 16.645 1.00 56.52 ATOM 83 C LYS A 401 14.522 -20.740 15.162 1.00 54.92 ATOM 84 O LYS A 401 15.488 -21.399 14.778 1.00 57.70 ATOM 85 CB LYS A 401 12.729 -21.308 16.823 1.00 59.81 ATOM 86 CG LYS A 401 12.536 -22.704 16.249 1.00 62.17 ATOM 87 N PHE A 402 13.782 -19.993 14.343 1.00 51.34 ATOM 88 CA PHE A 402 14.044 -19.962 12.919 1.00 51.22 ATOM 89 C PHE A 402 15.461 -19.473 12.592 1.00 48.13 ATOM 90 O PHE A 402 16.097 -19.991 11.666 1.00 46.65 ATOM 91 CB PHE A 402 12.985 -19.130 12.167 1.00 50.05 ATOM 92 CG PHE A 402 11.666 -19.852 11.995 1.00 53.27 ATOM 93 CD1 PHE A 402 11.626 -21.130 11.452 1.00 57.18 ATOM 94 CD2 PHE A 402 10.483 -19.271 12.387 1.00 53.62 ATOM 95 CE1 PHE A 402 10.420 -21.805 11.290 1.00 59.90 ATOM 96 CE2 PHE A 402 9.275 -19.941 12.229 1.00 56.01 ATOM 97 CZ PHE A 402 9.245 -21.208 11.684 1.00 57.76 ATOM 98 N LEU A 403 15.957 -18.500 13.350 1.00 46.16 ATOM 99 CA LEU A 403 17.328 -18.038 13.150 1.00 46.03 ATOM 100 C LEU A 403 18.346 -19.148 13.504 1.00 47.06 ATOM 101 O LEU A 403 19.319 -19.321 12.782 1.00 43.51 ATOM 102 CB LEU A 403 17.615 -16.733 13.917 1.00 46.22 ATOM 103 CG LEU A 403 19.106 -16.338 13.996 1.00 46.45 ATOM 104 CD1 LEU A 403 19.648 -16.011 12.613 1.00 42.68 ATOM 105 CD2 LEU A 403 19.347 -15.175 14.957 1.00 49.05 ATOM 106 N SER A 404 18.110 -19.913 14.579 1.00 48.85 ATOM 107 CA SER A 404 19.055 -20.955 14.981 1.00 51.04 ATOM 108 C SER A 404 19.093 -22.117 13.998 1.00 51.85 ATOM 109 O SER A 404 20.153 -22.713 13.759 1.00 48.62 ATOM 110 CB SER A 404 18.710 -21.523 16.367 1.00 55.18 ATOM 111 OG SER A 404 18.785 -20.517 17.340 1.00 57.23 ATOM 112 N GLN A 405 17.914 -22.504 13.523 1.00 53.50 ATOM 113 CA GLN A 405 17.794 -23.533 12.491 1.00 56.04 ATOM 114 C GLN A 405 18.549 -23.072 11.232 1.00 49.09 ATOM 115 O GLN A 405 19.254 -23.843 10.613 1.00 47.67 ATOM 116 CB GLN A 405 16.313 -23.784 12.139 1.00 58.97 ATOM 117 CG GLN A 405 15.536 -24.577 13.179 1.00 65.95 ATOM 118 CD GLN A 405 14.023 -24.520 12.970 1.00 69.10 ATOM 119 OE1 GLN A 405 13.485 -23.536 12.464 1.00 73.61 ATOM 120 NE2 GLN A 405 13.334 -25.574 13.376 1.00 72.05 ATOM 121 N HIS A 406 18.381 -21.811 10.876 1.00 44.07 ATOM 122 CA HIS A 406 19.083 -21.255 9.720 1.00 42.76 ATOM 123 C HIS A 406 20.573 -21.272 9.911 1.00 42.16 ATOM 124 O HIS A 406 21.301 -21.647 9.019 1.00 40.79 ATOM 125 CB HIS A 406 18.623 -19.851 9.435 1.00 39.50 ATOM 126 CG HIS A 406 19.558 -19.081 8.550 1.00 38.59 ATOM 127 ND1 HIS A 406 19.599 -19.250 7.203 1.00 38.08 ATOM 128 CD2 HIS A 406 20.518 -18.116 8.854 1.00 36.80 ATOM 129 CE1 HIS A 406 20.550 -18.444 6.687 1.00 35.13 ATOM 130 NE2 HIS A 406 21.113 -17.768 7.696 1.00 36.13 ATOM 131 N VAL A 407 21.035 -20.848 11.077 1.00 44.26 ATOM 132 CA VAL A 407 22.470 -20.770 11.327 1.00 46.80 ATOM 133 C VAL A 407 23.088 -22.147 11.286 1.00 48.04 ATOM 134 O VAL A 407 24.135 -22.343 10.711 1.00 50.91 ATOM 135 CB VAL A 407 22.775 -20.057 12.652 1.00 46.66 ATOM 136 CG1 VAL A 407 24.158 -20.427 13.169 1.00 47.96 ATOM 137 CG2 VAL A 407 22.670 -18.557 12.447 1.00 44.68 ATOM 138 N GLU A 408 22.391 -23.105 11.850 1.00 53.19 ATOM 139 CA GLU A 408 22.830 -24.484 11.837 1.00 56.74 ATOM 140 C GLU A 408 22.801 -25.191 10.477 1.00 57.23 ATOM 141 O GLU A 408 23.595 -26.107 10.247 1.00 61.28 ATOM 142 CB GLU A 408 22.023 -25.276 12.847 1.00 60.76 ATOM 143 CG GLU A 408 22.350 -24.865 14.271 1.00 65.96 ATOM 144 CD GLU A 408 22.342 -26.026 15.225 1.00 71.70 ATOM 145 OE1 GLU A 408 23.109 -26.982 14.983 1.00 71.46 ATOM 146 OE2 GLU A 408 21.575 -25.973 16.217 1.00 76.88 ATOM 147 N ARG A 409 21.884 -24.811 9.594 1.00 54.91 ATOM 148 CA ARG A 409 21.853 -25.401 8.245 1.00 51.90 ATOM 149 C ARG A 409 22.792 -24.692 7.269 1.00 48.01 ATOM 150 O ARG A 409 23.201 -25.286 6.272 1.00 47.38 ATOM 151 CB ARG A 409 20.427 -25.417 7.688 1.00 50.79 ATOM 152 CG ARG A 409 19.455 -26.235 8.528 1.00 55.44 ATOM 153 N ASN A 410 23.151 -23.435 7.555 1.00 45.20 ATOM 154 CA ASN A 410 23.876 -22.619 6.585 1.00 43.11 ATOM 155 C ASN A 410 25.255 -22.097 6.979 1.00 41.74 ATOM 156 O ASN A 410 25.996 -21.624 6.112 1.00 39.71 ATOM 157 CB ASN A 410 23.009 -21.445 6.181 1.00 44.81 ATOM 158 CG ASN A 410 21.744 -21.889 5.482 1.00 48.67 ATOM 159 OD1 ASN A 410 21.756 -22.144 4.290 1.00 53.21 ATOM 160 ND2 ASN A 410 20.662 -22.040 6.236 1.00 49.38 ATOM 161 N HIS A 411 25.605 -22.103 8.260 1.00 39.43 ATOM 162 CA HIS A 411 26.836 -21.396 8.661 1.00 39.12 ATOM 163 C HIS A 411 27.673 -22.106 9.687 1.00 40.90 ATOM 164 O HIS A 411 28.897 -22.117 9.580 1.00 40.37 ATOM 165 CB HIS A 411 26.526 -19.997 9.178 1.00 37.48 ATOM 166 CG HIS A 411 25.750 -19.128 8.227 1.00 36.06 ATOM 167 ND1 HIS A 411 26.257 -18.704 7.034 1.00 35.47 ATOM 168 CD2 HIS A 411 24.541 -18.469 8.384 1.00 35.64 ATOM 169 CE1 HIS A 411 25.401 -17.866 6.455 1.00 33.30 ATOM 170 NE2 HIS A 411 24.351 -17.717 7.269 1.00 35.06 ATOM 171 N SER A 412 27.041 -22.693 10.699 1.00 42.93 ATOM 172 CA SER A 412 27.783 -23.193 11.861 1.00 46.31 ATOM 173 C SER A 412 26.930 -24.133 12.705 1.00 48.86 ATOM 174 O SER A 412 25.886 -23.737 13.184 1.00 50.45 ATOM 175 CB SER A 412 28.232 -21.996 12.715 1.00 46.59 ATOM 176 OG SER A 412 29.133 -22.378 13.717 1.00 50.59 ATOM 177 N SER A 413 27.352 -25.383 12.846 1.00 53.44 ATOM 178 CA SER A 413 26.726 -26.328 13.795 1.00 59.43 ATOM 179 C SER A 413 27.776 -27.217 14.417 1.00 60.56 ATOM 180 O SER A 413 28.544 -27.836 13.694 1.00 60.73 ATOM 181 CB SER A 413 25.685 -27.204 13.097 1.00 62.63 ATOM 182 OG SER A 413 26.167 -27.661 11.842 1.00 66.16 ATOM 183 ZN ZN A 502 22.696 -16.399 7.373 1.00 38.32 ATOM 184 UNK UNX A 509 22.654 -12.933 2.050 1.00 30.00 ATOM 185 UNK UNX A 510 10.917 -12.431 8.918 1.00 30.00 ATOM 186 UNK UNX A 518 8.219 -15.570 18.378 1.00 30.00 TER