HEADER DNA BINDING PROTEIN 31-DEC-69 5Y3R TITLE Cryo-EM structure of Human DNA-PK Holoenzyme COMPND MOL_ID: 6; COMPND 2 MOLECULE: DNA-dependent protein kinase catalytic subunit; COMPND 3 CHAIN: C; COMPND 4 EC: 2.7.11.1; COMPND 5 FRAGMENT: UNP residues ; COMPND 6 ENGINEERED: YES; EXPDTA ELECTRON MICROSCOPY DBREF 5Y3R C 10 4128 UNP P78527 PRKDC_HUMAN 10 4128 SEQRES 1 C 32 GLY LEU SER GLU GLU THR GLN VAL LYS CYS LEU MET ASP SEQRES 2 C 32 GLN ALA THR ASP PRO ASN ILE LEU GLY ARG THR TRP GLU SEQRES 3 C 32 GLY TRP GLU PRO TRP MET ATOM 1 N GLY C4097 126.785 184.458 197.122 1.00121.21 ATOM 2 CA GLY C4097 127.199 184.430 198.507 1.00121.21 ATOM 3 C GLY C4097 128.665 184.748 198.680 1.00121.21 ATOM 4 O GLY C4097 129.014 185.720 199.352 1.00121.21 ATOM 5 N LEU C4098 129.532 183.959 198.057 1.00118.92 ATOM 6 CA LEU C4098 130.954 184.250 198.054 1.00118.92 ATOM 7 C LEU C4098 131.546 183.859 196.717 1.00118.92 ATOM 8 O LEU C4098 131.381 182.726 196.266 1.00118.92 ATOM 9 CB LEU C4098 131.683 183.507 199.170 1.00119.81 ATOM 10 CG LEU C4098 131.357 183.986 200.577 1.00119.81 ATOM 11 CD1 LEU C4098 132.003 183.082 201.603 1.00119.81 ATOM 12 CD2 LEU C4098 131.833 185.421 200.738 1.00119.81 ATOM 13 N SER C4099 132.270 184.785 196.111 1.00123.36 ATOM 14 CA SER C4099 132.986 184.502 194.881 1.00123.36 ATOM 15 C SER C4099 134.322 185.220 194.945 1.00123.36 ATOM 16 O SER C4099 134.349 186.418 195.234 1.00123.36 ATOM 17 CB SER C4099 132.171 184.971 193.670 1.00118.02 ATOM 18 OG SER C4099 130.909 184.329 193.625 1.00118.02 ATOM 19 N GLU C4100 135.431 184.501 194.765 1.00116.08 ATOM 20 CA GLU C4100 136.679 185.238 194.606 1.00116.08 ATOM 21 C GLU C4100 137.625 184.692 193.547 1.00116.08 ATOM 22 O GLU C4100 137.687 185.215 192.433 1.00116.08 ATOM 23 CB GLU C4100 137.358 185.334 195.971 1.00128.16 ATOM 24 CG GLU C4100 137.516 184.029 196.721 1.00128.16 ATOM 25 CD GLU C4100 137.900 184.261 198.167 1.00128.16 ATOM 26 OE1 GLU C4100 138.338 185.382 198.494 1.00128.16 ATOM 27 OE2 GLU C4100 137.749 183.333 198.984 1.00128.16 ATOM 28 N GLU C4101 138.340 183.622 193.863 1.00101.83 ATOM 29 CA GLU C4101 139.195 183.020 192.859 1.00101.83 ATOM 30 C GLU C4101 138.350 182.559 191.705 1.00101.83 ATOM 31 O GLU C4101 138.768 182.603 190.548 1.00101.83 ATOM 32 CB GLU C4101 139.949 181.872 193.488 1.00 94.31 ATOM 33 CG GLU C4101 139.018 180.845 194.042 1.00 94.31 ATOM 34 CD GLU C4101 139.730 179.859 194.908 1.00 94.31 ATOM 35 OE1 GLU C4101 140.976 179.838 194.873 1.00 94.31 ATOM 36 OE2 GLU C4101 139.052 179.095 195.620 1.00 94.31 ATOM 37 N THR C4102 137.141 182.151 192.034 1.00103.55 ATOM 38 CA THR C4102 136.024 182.157 191.124 1.00103.55 ATOM 39 C THR C4102 135.980 183.427 190.297 1.00103.55 ATOM 40 O THR C4102 136.177 183.396 189.076 1.00103.55 ATOM 41 CB THR C4102 134.787 182.076 191.983 1.00110.88 ATOM 42 OG1 THR C4102 134.751 183.268 192.768 1.00110.88 ATOM 43 CG2 THR C4102 134.927 180.925 192.933 1.00110.88 ATOM 44 N GLN C4103 135.717 184.555 190.974 1.00107.87 ATOM 45 CA GLN C4103 135.471 185.823 190.293 1.00107.87 ATOM 46 C GLN C4103 136.475 186.001 189.195 1.00107.87 ATOM 47 O GLN C4103 136.161 186.423 188.079 1.00107.87 ATOM 48 CB GLN C4103 135.618 186.993 191.253 1.00114.17 ATOM 49 CG GLN C4103 134.555 187.236 192.245 1.00114.17 ATOM 50 CD GLN C4103 135.013 188.287 193.229 1.00114.17 ATOM 51 OE1 GLN C4103 136.186 188.326 193.599 1.00114.17 ATOM 52 NE2 GLN C4103 134.118 189.189 193.597 1.00114.17 ATOM 53 N VAL C4104 137.716 185.702 189.528 1.00103.85 ATOM 54 CA VAL C4104 138.715 185.532 188.500 1.00103.85 ATOM 55 C VAL C4104 138.168 184.599 187.444 1.00103.85 ATOM 56 O VAL C4104 137.730 185.032 186.374 1.00103.85 ATOM 57 CB VAL C4104 139.997 184.966 189.115 1.00105.85 ATOM 58 CG1 VAL C4104 141.155 185.123 188.151 1.00105.85 ATOM 59 CG2 VAL C4104 140.218 185.552 190.511 1.00105.85 ATOM 60 N LYS C4105 138.030 183.329 187.826 1.00104.21 ATOM 61 CA LYS C4105 137.850 182.248 186.872 1.00104.21 ATOM 62 C LYS C4105 136.897 182.681 185.787 1.00104.21 ATOM 63 O LYS C4105 137.269 182.815 184.615 1.00104.21 ATOM 64 CB LYS C4105 137.288 181.019 187.575 1.00 96.14 ATOM 65 CG LYS C4105 138.110 180.495 188.686 1.00 96.14 ATOM 66 CD LYS C4105 137.395 179.407 189.423 1.00 96.14 ATOM 67 CE LYS C4105 138.165 178.980 190.643 1.00 96.14 ATOM 68 NZ LYS C4105 137.480 177.932 191.435 1.00 96.14 ATOM 69 N CYS C4106 135.657 182.939 186.186 1.00113.49 ATOM 70 CA CYS C4106 134.697 183.515 185.263 1.00113.49 ATOM 71 C CYS C4106 135.278 184.726 184.574 1.00113.49 ATOM 72 O CYS C4106 135.645 184.658 183.403 1.00113.49 ATOM 73 CB CYS C4106 133.421 183.895 186.005 1.00126.09 ATOM 74 SG CYS C4106 133.727 184.861 187.476 1.00126.09 ATOM 75 N LEU C4107 135.486 185.806 185.324 1.00105.83 ATOM 76 CA LEU C4107 135.718 187.093 184.688 1.00105.83 ATOM 77 C LEU C4107 136.740 186.989 183.591 1.00105.83 ATOM 78 O LEU C4107 136.707 187.757 182.628 1.00105.83 ATOM 79 CB LEU C4107 136.144 188.122 185.709 1.00103.03 ATOM 80 CG LEU C4107 134.950 188.971 186.138 1.00103.03 ATOM 81 CD1 LEU C4107 133.915 188.168 186.882 1.00103.03 ATOM 82 CD2 LEU C4107 135.358 190.186 186.940 1.00103.03 ATOM 83 N MET C4108 137.597 185.996 183.682 1.00107.72 ATOM 84 CA MET C4108 138.561 185.720 182.652 1.00107.72 ATOM 85 C MET C4108 137.857 185.437 181.347 1.00107.72 ATOM 86 O MET C4108 137.841 186.265 180.435 1.00107.72 ATOM 87 CB MET C4108 139.379 184.518 183.065 1.00107.63 ATOM 88 CG MET C4108 139.873 184.636 184.469 1.00107.63 ATOM 89 SD MET C4108 140.809 186.150 184.732 1.00107.63 ATOM 90 CE MET C4108 139.629 187.222 185.572 1.00107.63 ATOM 91 N ASP C4109 137.247 184.274 181.265 1.00119.17 ATOM 92 CA ASP C4109 136.706 183.799 180.008 1.00119.17 ATOM 93 C ASP C4109 135.235 184.070 179.851 1.00119.17 ATOM 94 O ASP C4109 134.620 183.604 178.888 1.00119.17 ATOM 95 CB ASP C4109 137.024 182.332 179.834 1.00126.25 ATOM 96 CG ASP C4109 138.434 182.140 179.390 1.00126.25 ATOM 97 OD1 ASP C4109 139.037 183.155 178.985 1.00126.25 ATOM 98 OD2 ASP C4109 138.937 181.004 179.418 1.00126.25 ATOM 99 N GLN C4110 134.646 184.803 180.781 1.00124.92 ATOM 100 CA GLN C4110 133.504 185.596 180.385 1.00124.92 ATOM 101 C GLN C4110 133.852 186.281 179.079 1.00124.92 ATOM 102 O GLN C4110 133.146 186.146 178.076 1.00124.92 ATOM 103 CB GLN C4110 133.185 186.635 181.462 1.00128.33 ATOM 104 CG GLN C4110 132.793 186.090 182.828 1.00128.33 ATOM 105 CD GLN C4110 132.548 187.207 183.840 1.00128.33 ATOM 106 OE1 GLN C4110 133.075 188.311 183.696 1.00128.33 ATOM 107 NE2 GLN C4110 131.745 186.925 184.861 1.00128.33 ATOM 108 N ALA C4111 135.014 186.932 179.058 1.00116.52 ATOM 109 CA ALA C4111 135.469 187.613 177.861 1.00116.52 ATOM 110 C ALA C4111 135.743 186.640 176.735 1.00116.52 ATOM 111 O ALA C4111 135.528 186.980 175.572 1.00116.52 ATOM 112 CB ALA C4111 136.722 188.424 178.167 1.00111.79 ATOM 113 N THR C4112 136.174 185.421 177.045 1.00119.14 ATOM 114 CA THR C4112 136.489 184.525 175.946 1.00119.14 ATOM 115 C THR C4112 135.279 184.264 175.082 1.00119.14 ATOM 116 O THR C4112 135.405 183.660 174.016 1.00119.14 ATOM 117 CB THR C4112 137.006 183.183 176.437 1.00123.08 ATOM 118 OG1 THR C4112 137.778 182.590 175.396 1.00123.08 ATOM 119 CG2 THR C4112 135.854 182.236 176.667 1.00123.08 ATOM 120 N ASP C4113 134.140 184.713 175.501 1.00122.07 ATOM 121 CA ASP C4113 132.934 184.188 174.935 1.00122.07 ATOM 122 C ASP C4113 132.672 184.834 173.586 1.00122.07 ATOM 123 O ASP C4113 132.306 186.004 173.530 1.00122.07 ATOM 124 CB ASP C4113 131.800 184.459 175.903 1.00126.95 ATOM 125 CG ASP C4113 130.580 183.727 175.548 1.00126.95 ATOM 126 OD1 ASP C4113 130.666 182.892 174.632 1.00126.95 ATOM 127 OD2 ASP C4113 129.530 183.993 176.167 1.00126.95 ATOM 128 N PRO C4114 132.810 184.103 172.486 1.00125.37 ATOM 129 CA PRO C4114 132.423 184.673 171.186 1.00125.37 ATOM 130 C PRO C4114 131.058 185.303 171.250 1.00125.37 ATOM 131 O PRO C4114 130.825 186.406 170.744 1.00125.37 ATOM 132 CB PRO C4114 132.443 183.453 170.259 1.00128.04 ATOM 133 CG PRO C4114 132.227 182.302 171.174 1.00128.04 ATOM 134 CD PRO C4114 132.990 182.650 172.408 1.00128.04 ATOM 135 N ASN C4115 130.156 184.603 171.928 1.00128.18 ATOM 136 CA ASN C4115 128.911 185.145 172.430 1.00128.18 ATOM 137 C ASN C4115 129.143 186.516 173.062 1.00128.18 ATOM 138 O ASN C4115 128.562 187.510 172.622 1.00128.18 ATOM 139 CB ASN C4115 128.352 184.115 173.403 1.00128.22 ATOM 140 CG ASN C4115 126.960 184.360 173.816 1.00128.22 ATOM 141 OD1 ASN C4115 126.154 184.914 173.084 1.00128.22 ATOM 142 ND2 ASN C4115 126.647 183.910 175.019 1.00128.22 ATOM 143 N ILE C4116 129.994 186.610 174.089 1.00123.97 ATOM 144 CA ILE C4116 130.298 187.951 174.590 1.00123.97 ATOM 145 C ILE C4116 131.105 188.748 173.572 1.00123.97 ATOM 146 O ILE C4116 131.058 189.983 173.576 1.00123.97 ATOM 147 CB ILE C4116 131.065 187.939 175.928 1.00122.30 ATOM 148 CG1 ILE C4116 130.912 189.287 176.628 1.00122.30 ATOM 149 CG2 ILE C4116 132.556 187.851 175.699 1.00122.30 ATOM 150 CD1 ILE C4116 131.476 189.320 178.031 1.00122.30 ATOM 151 N LEU C4117 131.832 188.079 172.680 1.00119.51 ATOM 152 CA LEU C4117 132.865 188.780 171.921 1.00119.51 ATOM 153 C LEU C4117 132.294 189.630 170.793 1.00119.51 ATOM 154 O LEU C4117 132.404 190.859 170.817 1.00119.51 ATOM 155 CB LEU C4117 133.900 187.777 171.416 1.00116.86 ATOM 156 CG LEU C4117 134.721 187.396 172.640 1.00116.86 ATOM 157 CD1 LEU C4117 135.654 186.268 172.383 1.00116.86 ATOM 158 CD2 LEU C4117 135.487 188.623 173.072 1.00116.86 ATOM 159 N GLY C4118 131.664 189.004 169.804 1.00120.13 ATOM 160 CA GLY C4118 131.240 189.782 168.658 1.00120.13 ATOM 161 C GLY C4118 130.243 190.864 168.985 1.00120.13 ATOM 162 O GLY C4118 129.909 191.664 168.105 1.00120.13 ATOM 163 N ARG C4119 129.778 190.922 170.228 1.00128.48 ATOM 164 CA ARG C4119 128.890 191.995 170.645 1.00128.48 ATOM 165 C ARG C4119 129.641 193.306 170.810 1.00128.48 ATOM 166 O ARG C4119 129.378 194.274 170.093 1.00128.48 ATOM 167 CB ARG C4119 128.192 191.634 171.958 1.00139.03 ATOM 168 CG ARG C4119 127.150 190.526 171.880 1.00139.03 ATOM 169 CD ARG C4119 126.003 190.938 170.971 1.00139.03 ATOM 170 NE ARG C4119 125.393 192.203 171.369 1.00139.03 ATOM 171 CZ ARG C4119 124.370 192.351 172.205 1.00139.03 ATOM 172 NH1 ARG C4119 123.760 191.309 172.754 1.00139.03 ATOM 173 NH2 ARG C4119 123.941 193.570 172.454 1.00139.03 ATOM 174 N THR C4120 130.601 193.334 171.737 1.00130.22 ATOM 175 CA THR C4120 131.029 194.572 172.383 1.00130.22 ATOM 176 C THR C4120 131.207 195.724 171.396 1.00130.22 ATOM 177 O THR C4120 130.388 196.649 171.365 1.00130.22 ATOM 178 CB THR C4120 132.313 194.304 173.166 1.00129.18 ATOM 179 OG1 THR C4120 132.018 193.458 174.287 1.00129.18 ATOM 180 CG2 THR C4120 132.943 195.591 173.639 1.00129.18 ATOM 181 N TRP C4121 132.240 195.666 170.552 1.00129.57 ATOM 182 CA TRP C4121 132.468 196.718 169.565 1.00129.57 ATOM 183 C TRP C4121 133.702 196.404 168.728 1.00129.57 ATOM 184 O TRP C4121 134.618 195.707 169.172 1.00129.57 ATOM 185 CB TRP C4121 132.616 198.092 170.238 1.00127.62 ATOM 186 CG TRP C4121 133.085 199.136 169.328 1.00127.62 ATOM 187 CD1 TRP C4121 134.209 199.883 169.456 1.00127.62 ATOM 188 CD2 TRP C4121 132.510 199.483 168.070 1.00127.62 ATOM 189 NE1 TRP C4121 134.334 200.730 168.388 1.00127.62 ATOM 190 CE2 TRP C4121 133.315 200.485 167.509 1.00127.62 ATOM 191 CE3 TRP C4121 131.387 199.046 167.366 1.00127.62 ATOM 192 CZ2 TRP C4121 133.026 201.071 166.287 1.00127.62 ATOM 193 CZ3 TRP C4121 131.104 199.623 166.156 1.00127.62 ATOM 194 CH2 TRP C4121 131.917 200.627 165.626 1.00127.62 ATOM 195 N GLU C4122 133.736 196.984 167.524 1.00128.29 ATOM 196 CA GLU C4122 134.801 196.713 166.566 1.00128.29 ATOM 197 C GLU C4122 136.063 197.498 166.873 1.00128.29 ATOM 198 O GLU C4122 137.166 196.955 166.764 1.00128.29 ATOM 199 CB GLU C4122 134.319 197.011 165.148 1.00134.99 ATOM 200 CG GLU C4122 133.367 195.965 164.629 1.00134.99 ATOM 201 CD GLU C4122 132.747 196.311 163.291 1.00134.99 ATOM 202 OE1 GLU C4122 132.904 197.459 162.832 1.00134.99 ATOM 203 OE2 GLU C4122 132.087 195.427 162.709 1.00134.99 ATOM 204 N GLY C4123 135.928 198.764 167.266 1.00118.09 ATOM 205 CA GLY C4123 137.097 199.571 167.569 1.00118.09 ATOM 206 C GLY C4123 137.981 198.958 168.626 1.00118.09 ATOM 207 O GLY C4123 139.129 199.377 168.790 1.00118.09 ATOM 208 N TRP C4124 137.473 197.972 169.345 1.00115.60 ATOM 209 CA TRP C4124 138.282 197.201 170.263 1.00115.60 ATOM 210 C TRP C4124 138.892 195.971 169.624 1.00115.60 ATOM 211 O TRP C4124 139.727 195.318 170.252 1.00115.60 ATOM 212 CB TRP C4124 137.454 196.849 171.491 1.00109.34 ATOM 213 CG TRP C4124 137.459 198.011 172.364 1.00109.34 ATOM 214 CD1 TRP C4124 138.014 199.197 172.070 1.00109.34 ATOM 215 CD2 TRP C4124 136.989 198.109 173.709 1.00109.34 ATOM 216 NE1 TRP C4124 137.907 200.051 173.125 1.00109.34 ATOM 217 CE2 TRP C4124 137.287 199.403 174.153 1.00109.34 ATOM 218 CE3 TRP C4124 136.340 197.236 174.577 1.00109.34 ATOM 219 CZ2 TRP C4124 136.956 199.853 175.413 1.00109.34 ATOM 220 CZ3 TRP C4124 136.022 197.682 175.824 1.00109.34 ATOM 221 CH2 TRP C4124 136.316 198.985 176.226 1.00109.34 ATOM 222 N GLU C4125 138.496 195.657 168.401 1.00128.83 ATOM 223 CA GLU C4125 138.985 194.557 167.578 1.00128.83 ATOM 224 C GLU C4125 139.381 193.288 168.311 1.00128.83 ATOM 225 O GLU C4125 140.507 192.816 168.131 1.00128.83 ATOM 226 CB GLU C4125 140.192 194.978 166.753 1.00129.27 ATOM 227 CG GLU C4125 139.904 195.944 165.659 1.00129.27 ATOM 228 CD GLU C4125 141.134 196.217 164.841 1.00129.27 ATOM 229 OE1 GLU C4125 142.223 195.775 165.260 1.00129.27 ATOM 230 OE2 GLU C4125 141.021 196.857 163.777 1.00129.27 ATOM 231 N PRO C4126 138.524 192.692 169.132 1.00132.67 ATOM 232 CA PRO C4126 138.689 191.259 169.360 1.00132.67 ATOM 233 C PRO C4126 138.320 190.488 168.121 1.00132.67 ATOM 234 O PRO C4126 138.858 189.400 167.886 1.00132.67 ATOM 235 CB PRO C4126 137.736 190.973 170.520 1.00133.08 ATOM 236 CG PRO C4126 136.675 191.978 170.356 1.00133.08 ATOM 237 CD PRO C4126 137.320 193.211 169.799 1.00133.08 ATOM 238 N TRP C4127 137.420 191.047 167.310 1.00133.32 ATOM 239 CA TRP C4127 137.098 190.446 166.026 1.00133.32 ATOM 240 C TRP C4127 138.337 190.367 165.161 1.00133.32 ATOM 241 O TRP C4127 138.466 189.466 164.327 1.00133.32 ATOM 242 CB TRP C4127 136.036 191.266 165.308 1.00126.32 ATOM 243 CG TRP C4127 136.561 192.586 164.927 1.00126.32 ATOM 244 CD1 TRP C4127 136.527 193.725 165.660 1.00126.32 ATOM 245 CD2 TRP C4127 137.252 192.898 163.724 1.00126.32 ATOM 246 NE1 TRP C4127 137.137 194.742 164.976 1.00126.32 ATOM 247 CE2 TRP C4127 137.599 194.253 163.784 1.00126.32 ATOM 248 CE3 TRP C4127 137.601 192.162 162.597 1.00126.32 ATOM 249 CZ2 TRP C4127 138.276 194.889 162.758 1.00126.32 ATOM 250 CZ3 TRP C4127 138.277 192.784 161.597 1.00126.32 ATOM 251 CH2 TRP C4127 138.601 194.138 161.669 1.00126.32 ATOM 252 N MET C4128 139.243 191.320 165.321 1.00130.65 ATOM 253 CA MET C4128 140.494 191.246 164.614 1.00130.65 ATOM 254 C MET C4128 141.572 191.159 165.674 1.00130.65 ATOM 255 O MET C4128 141.313 190.673 166.776 1.00130.65 ATOM 256 CB MET C4128 140.702 192.447 163.701 1.00129.78 ATOM 257 CG MET C4128 141.803 192.227 162.679 1.00129.78 ATOM 258 SD MET C4128 141.965 193.507 161.419 1.00129.78 ATOM 259 CE MET C4128 142.814 194.774 162.343 1.00129.78 TER