HEADER LIGASE 31-DEC-69 8D80 TITLE Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3 COMPND MOL_ID: 2; COMPND 2 MOLECULE: Protein cereblon; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 3; COMPND 6 DNA-binding protein Ikaros; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; EXPDTA ELECTRON MICROSCOPY DBREF 8D80 B 1 442 UNP Q96SW2 CRBN_HUMAN 1 442 DBREF 8D80 C 112 196 UNP Q13422 IKZF1_HUMAN 112 196 SEQRES 1 C 29 GLY GLU ARG PRO PHE GLN CYS ASN GLN CYS GLY ALA SER SEQRES 2 C 29 PHE THR GLN LYS GLY ASN LEU LEU ARG HIS ILE LYS LEU SEQRES 3 C 29 HIS SER GLY ATOM 1 N GLY C 141 106.700 207.158 144.351 1.00293.26 ATOM 2 CA GLY C 141 105.261 207.031 144.493 1.00293.26 ATOM 3 C GLY C 141 104.773 205.605 144.339 1.00293.26 ATOM 4 O GLY C 141 105.570 204.667 144.314 1.00293.26 ATOM 5 N GLU C 142 103.452 205.440 144.238 1.00287.12 ATOM 6 CA GLU C 142 102.887 204.103 144.087 1.00287.12 ATOM 7 C GLU C 142 103.167 203.523 142.705 1.00287.12 ATOM 8 O GLU C 142 103.245 202.297 142.561 1.00287.12 ATOM 9 CB GLU C 142 101.386 204.132 144.381 1.00287.12 ATOM 10 CG GLU C 142 100.611 205.217 143.652 1.00287.12 ATOM 11 CD GLU C 142 100.045 204.747 142.330 1.00287.12 ATOM 12 OE1 GLU C 142 99.976 203.518 142.114 1.00287.12 ATOM 13 OE2 GLU C 142 99.659 205.607 141.511 1.00287.12 ATOM 14 N ARG C 143 103.321 204.385 141.685 1.00285.73 ATOM 15 CA ARG C 143 103.762 204.061 140.325 1.00285.73 ATOM 16 C ARG C 143 103.110 202.785 139.799 1.00285.73 ATOM 17 O ARG C 143 103.754 201.729 139.737 1.00285.73 ATOM 18 CB ARG C 143 105.296 203.981 140.246 1.00285.73 ATOM 19 CG ARG C 143 106.008 203.076 141.248 1.00285.73 ATOM 20 CD ARG C 143 107.490 203.403 141.310 1.00285.73 ATOM 21 NE ARG C 143 108.223 202.483 142.171 1.00285.73 ATOM 22 CZ ARG C 143 108.957 201.471 141.728 1.00285.73 ATOM 23 NH1 ARG C 143 109.087 201.227 140.434 1.00285.73 ATOM 24 NH2 ARG C 143 109.581 200.689 142.604 1.00285.73 ATOM 25 N PRO C 144 101.833 202.844 139.409 1.00284.69 ATOM 26 CA PRO C 144 101.107 201.613 139.051 1.00284.69 ATOM 27 C PRO C 144 101.683 200.874 137.854 1.00284.69 ATOM 28 O PRO C 144 101.340 199.701 137.660 1.00284.69 ATOM 29 CB PRO C 144 99.688 202.118 138.756 1.00284.69 ATOM 30 CG PRO C 144 99.889 203.529 138.311 1.00284.69 ATOM 31 CD PRO C 144 101.050 204.056 139.112 1.00284.69 ATOM 32 N PHE C 145 102.525 201.515 137.046 1.00280.00 ATOM 33 CA PHE C 145 103.130 200.845 135.902 1.00280.00 ATOM 34 C PHE C 145 103.966 199.661 136.371 1.00280.00 ATOM 35 O PHE C 145 104.774 199.788 137.297 1.00280.00 ATOM 36 CB PHE C 145 103.994 201.826 135.109 1.00280.00 ATOM 37 CG PHE C 145 103.396 203.200 134.979 1.00280.00 ATOM 38 CD1 PHE C 145 103.652 204.176 135.929 1.00280.00 ATOM 39 CD2 PHE C 145 102.579 203.514 133.907 1.00280.00 ATOM 40 CE1 PHE C 145 103.103 205.439 135.811 1.00280.00 ATOM 41 CE2 PHE C 145 102.028 204.775 133.783 1.00280.00 ATOM 42 CZ PHE C 145 102.290 205.739 134.737 1.00280.00 ATOM 43 N GLN C 146 103.771 198.509 135.732 1.00251.55 ATOM 44 CA GLN C 146 104.468 197.291 136.124 1.00251.55 ATOM 45 C GLN C 146 104.461 196.318 134.956 1.00251.55 ATOM 46 O GLN C 146 103.411 196.081 134.351 1.00251.55 ATOM 47 CB GLN C 146 103.814 196.651 137.354 1.00251.55 ATOM 48 CG GLN C 146 104.583 195.469 137.915 1.00251.55 ATOM 49 CD GLN C 146 105.878 195.883 138.581 1.00251.55 ATOM 50 OE1 GLN C 146 105.935 196.892 139.283 1.00251.55 ATOM 51 NE2 GLN C 146 106.930 195.105 138.360 1.00251.55 ATOM 52 N CYS C 147 105.628 195.758 134.648 1.00246.79 ATOM 53 CA CYS C 147 105.723 194.769 133.584 1.00246.79 ATOM 54 C CYS C 147 105.182 193.426 134.063 1.00246.79 ATOM 55 O CYS C 147 105.526 192.951 135.148 1.00246.79 ATOM 56 CB CYS C 147 107.174 194.626 133.122 1.00246.79 ATOM 57 SG CYS C 147 107.409 193.553 131.688 1.00246.79 ATOM 58 N ASN C 148 104.330 192.812 133.243 1.00215.60 ATOM 59 CA ASN C 148 103.682 191.552 133.592 1.00215.60 ATOM 60 C ASN C 148 104.470 190.330 133.140 1.00215.60 ATOM 61 O ASN C 148 104.675 189.403 133.930 1.00215.60 ATOM 62 CB ASN C 148 102.275 191.498 132.990 1.00215.60 ATOM 63 CG ASN C 148 101.392 192.631 133.473 1.00215.60 ATOM 64 OD1 ASN C 148 101.500 193.070 134.618 1.00215.60 ATOM 65 ND2 ASN C 148 100.510 193.108 132.602 1.00215.60 ATOM 66 N GLN C 149 105.007 190.389 131.921 1.00214.97 ATOM 67 CA GLN C 149 105.852 189.279 131.413 1.00214.97 ATOM 68 C GLN C 149 107.096 189.127 132.290 1.00214.97 ATOM 69 O GLN C 149 107.343 187.997 132.755 1.00214.97 ATOM 70 CB GLN C 149 106.241 189.509 129.956 1.00214.97 ATOM 71 CG GLN C 149 106.550 188.216 129.217 1.00214.97 ATOM 72 CD GLN C 149 105.807 187.036 129.795 1.00214.97 ATOM 73 OE1 GLN C 149 104.843 186.546 129.215 1.00214.97 ATOM 74 NE2 GLN C 149 106.255 186.568 130.949 1.00214.97 ATOM 75 N CYS C 150 107.849 190.207 132.504 1.00241.97 ATOM 76 CA CYS C 150 109.118 190.054 133.261 1.00241.97 ATOM 77 C CYS C 150 108.932 190.424 134.734 1.00241.97 ATOM 78 O CYS C 150 109.487 189.709 135.589 1.00241.97 ATOM 79 CB CYS C 150 110.223 190.913 132.673 1.00241.97 ATOM 80 SG CYS C 150 110.688 192.287 133.754 1.00241.97 ATOM 81 N GLY C 151 108.205 191.504 135.020 1.00219.28 ATOM 82 CA GLY C 151 108.079 191.944 136.421 1.00219.28 ATOM 83 C GLY C 151 108.911 193.176 136.695 1.00219.28 ATOM 84 O GLY C 151 109.171 193.459 137.881 1.00219.28 ATOM 85 N ALA C 152 109.309 193.886 135.635 1.00241.08 ATOM 86 CA ALA C 152 110.107 195.126 135.791 1.00241.08 ATOM 87 C ALA C 152 109.186 196.257 136.245 1.00241.08 ATOM 88 O ALA C 152 107.999 196.252 135.864 1.00241.08 ATOM 89 CB ALA C 152 110.790 195.478 134.495 1.00241.08 ATOM 90 N SER C 153 109.719 197.191 137.033 1.00267.89 ATOM 91 CA SER C 153 108.865 198.255 137.537 1.00267.89 ATOM 92 C SER C 153 109.322 199.593 136.975 1.00267.89 ATOM 93 O SER C 153 110.524 199.870 136.904 1.00267.89 ATOM 94 CB SER C 153 108.883 198.295 139.067 1.00267.89 ATOM 95 OG SER C 153 107.776 199.021 139.573 1.00267.89 ATOM 96 N PHE C 154 108.359 200.419 136.574 1.00278.87 ATOM 97 CA PHE C 154 108.649 201.723 135.999 1.00278.87 ATOM 98 C PHE C 154 107.721 202.762 136.608 1.00278.87 ATOM 99 O PHE C 154 106.593 202.454 137.002 1.00278.87 ATOM 100 CB PHE C 154 108.487 201.722 134.473 1.00278.87 ATOM 101 CG PHE C 154 109.202 200.595 133.786 1.00278.87 ATOM 102 CD1 PHE C 154 110.547 200.696 133.477 1.00278.87 ATOM 103 CD2 PHE C 154 108.524 199.439 133.439 1.00278.87 ATOM 104 CE1 PHE C 154 111.206 199.660 132.840 1.00278.87 ATOM 105 CE2 PHE C 154 109.176 198.400 132.802 1.00278.87 ATOM 106 CZ PHE C 154 110.518 198.511 132.502 1.00278.87 ATOM 107 N THR C 155 108.209 204.000 136.683 1.00281.97 ATOM 108 CA THR C 155 107.383 205.118 137.114 1.00281.97 ATOM 109 C THR C 155 106.768 205.886 135.953 1.00281.97 ATOM 110 O THR C 155 105.997 206.823 136.190 1.00281.97 ATOM 111 CB THR C 155 108.197 206.083 137.987 1.00281.97 ATOM 112 OG1 THR C 155 107.342 207.123 138.479 1.00281.97 ATOM 113 CG2 THR C 155 109.334 206.702 137.192 1.00281.97 ATOM 114 N GLN C 156 107.087 205.517 134.714 1.00292.89 ATOM 115 CA GLN C 156 106.503 206.111 133.522 1.00292.89 ATOM 116 C GLN C 156 106.029 205.006 132.576 1.00292.89 ATOM 117 O GLN C 156 106.054 203.816 132.911 1.00292.89 ATOM 118 CB GLN C 156 107.509 207.054 132.854 1.00292.89 ATOM 119 CG GLN C 156 108.609 206.361 132.062 1.00292.89 ATOM 120 CD GLN C 156 109.801 205.984 132.919 1.00292.89 ATOM 121 OE1 GLN C 156 109.697 205.882 134.139 1.00292.89 ATOM 122 NE2 GLN C 156 110.946 205.784 132.280 1.00292.89 ATOM 123 N LYS C 157 105.590 205.407 131.383 1.00289.06 ATOM 124 CA LYS C 157 105.038 204.481 130.402 1.00289.06 ATOM 125 C LYS C 157 105.973 204.179 129.239 1.00289.06 ATOM 126 O LYS C 157 105.859 203.108 128.639 1.00289.06 ATOM 127 CB LYS C 157 103.712 205.028 129.851 1.00289.06 ATOM 128 CG LYS C 157 102.991 204.111 128.871 1.00289.06 ATOM 129 CD LYS C 157 102.728 202.738 129.471 1.00289.06 ATOM 130 CE LYS C 157 101.672 202.799 130.559 1.00289.06 ATOM 131 NZ LYS C 157 101.380 201.451 131.121 1.00289.06 ATOM 132 N GLY C 158 106.899 205.083 128.913 1.00296.51 ATOM 133 CA GLY C 158 107.749 204.865 127.751 1.00296.51 ATOM 134 C GLY C 158 108.622 203.632 127.881 1.00296.51 ATOM 135 O GLY C 158 108.701 202.808 126.965 1.00296.51 ATOM 136 N ASN C 159 109.282 203.478 129.032 1.00300.07 ATOM 137 CA ASN C 159 110.121 202.303 129.236 1.00300.07 ATOM 138 C ASN C 159 109.292 201.032 129.346 1.00300.07 ATOM 139 O ASN C 159 109.737 199.967 128.906 1.00300.07 ATOM 140 CB ASN C 159 110.997 202.480 130.476 1.00300.07 ATOM 141 CG ASN C 159 112.120 203.472 130.256 1.00300.07 ATOM 142 OD1 ASN C 159 112.322 203.960 129.144 1.00300.07 ATOM 143 ND2 ASN C 159 112.869 203.764 131.313 1.00300.07 ATOM 144 N LEU C 160 108.090 201.118 129.920 1.00293.82 ATOM 145 CA LEU C 160 107.216 199.950 129.975 1.00293.82 ATOM 146 C LEU C 160 106.827 199.495 128.573 1.00293.82 ATOM 147 O LEU C 160 106.833 198.297 128.271 1.00293.82 ATOM 148 CB LEU C 160 105.974 200.262 130.813 1.00293.82 ATOM 149 CG LEU C 160 105.026 199.097 131.110 1.00293.82 ATOM 150 CD1 LEU C 160 104.509 199.185 132.536 1.00293.82 ATOM 151 CD2 LEU C 160 103.863 199.068 130.126 1.00293.82 ATOM 152 N LEU C 161 106.492 200.446 127.697 1.00286.92 ATOM 153 CA LEU C 161 106.168 200.102 126.315 1.00286.92 ATOM 154 C LEU C 161 107.382 199.537 125.586 1.00286.92 ATOM 155 O LEU C 161 107.260 198.576 124.813 1.00286.92 ATOM 156 CB LEU C 161 105.626 201.331 125.587 1.00286.92 ATOM 157 CG LEU C 161 104.280 201.872 126.073 1.00286.92 ATOM 158 CD1 LEU C 161 103.939 203.177 125.370 1.00286.92 ATOM 159 CD2 LEU C 161 103.180 200.842 125.863 1.00286.92 ATOM 160 N ARG C 162 108.559 200.123 125.818 1.00287.06 ATOM 161 CA ARG C 162 109.778 199.601 125.209 1.00287.06 ATOM 162 C ARG C 162 110.029 198.163 125.644 1.00287.06 ATOM 163 O ARG C 162 110.378 197.308 124.823 1.00287.06 ATOM 164 CB ARG C 162 110.967 200.489 125.573 1.00287.06 ATOM 165 CG ARG C 162 112.274 200.087 124.908 1.00287.06 ATOM 166 CD ARG C 162 113.390 201.069 125.237 1.00287.06 ATOM 167 NE ARG C 162 113.712 201.079 126.659 1.00287.06 ATOM 168 CZ ARG C 162 114.547 200.232 127.246 1.00287.06 ATOM 169 NH1 ARG C 162 115.167 199.285 126.559 1.00287.06 ATOM 170 NH2 ARG C 162 114.765 200.336 128.553 1.00287.06 ATOM 171 N HIS C 163 109.831 197.874 126.930 1.00293.21 ATOM 172 CA HIS C 163 110.022 196.519 127.431 1.00293.21 ATOM 173 C HIS C 163 108.956 195.566 126.899 1.00293.21 ATOM 174 O HIS C 163 109.240 194.383 126.678 1.00293.21 ATOM 175 CB HIS C 163 110.024 196.534 128.959 1.00293.21 ATOM 176 CG HIS C 163 110.435 195.237 129.577 1.00293.21 ATOM 177 ND1 HIS C 163 111.216 194.313 128.918 1.00293.21 ATOM 178 CD2 HIS C 163 110.193 194.718 130.804 1.00293.21 ATOM 179 CE1 HIS C 163 111.429 193.275 129.708 1.00293.21 ATOM 180 NE2 HIS C 163 110.817 193.496 130.858 1.00293.21 ATOM 181 N ILE C 164 107.732 196.055 126.688 1.00280.19 ATOM 182 CA ILE C 164 106.687 195.212 126.109 1.00280.19 ATOM 183 C ILE C 164 107.051 194.817 124.682 1.00280.19 ATOM 184 O ILE C 164 106.948 193.645 124.298 1.00280.19 ATOM 185 CB ILE C 164 105.322 195.920 126.171 1.00280.19 ATOM 186 CG1 ILE C 164 104.793 195.939 127.607 1.00280.19 ATOM 187 CG2 ILE C 164 104.328 195.246 125.236 1.00280.19 ATOM 188 CD1 ILE C 164 104.198 194.618 128.060 1.00280.19 ATOM 189 N LYS C 165 107.486 195.788 123.872 1.00276.62 ATOM 190 CA LYS C 165 107.955 195.444 122.531 1.00276.62 ATOM 191 C LYS C 165 109.219 194.593 122.554 1.00276.62 ATOM 192 O LYS C 165 109.439 193.812 121.622 1.00276.62 ATOM 193 CB LYS C 165 108.192 196.695 121.678 1.00276.62 ATOM 194 CG LYS C 165 106.980 197.133 120.857 1.00276.62 ATOM 195 CD LYS C 165 105.929 197.881 121.650 1.00276.62 ATOM 196 CE LYS C 165 106.377 199.301 121.938 1.00276.62 ATOM 197 NZ LYS C 165 105.321 200.070 122.647 1.00276.62 ATOM 198 N LEU C 166 110.053 194.731 123.585 1.00259.93 ATOM 199 CA LEU C 166 111.198 193.840 123.737 1.00259.93 ATOM 200 C LEU C 166 110.749 192.403 123.973 1.00259.93 ATOM 201 O LEU C 166 111.304 191.467 123.386 1.00259.93 ATOM 202 CB LEU C 166 112.075 194.324 124.889 1.00259.93 ATOM 203 CG LEU C 166 112.994 193.314 125.573 1.00259.93 ATOM 204 CD1 LEU C 166 114.057 192.777 124.619 1.00259.93 ATOM 205 CD2 LEU C 166 113.623 193.953 126.791 1.00259.93 ATOM 206 N HIS C 167 109.750 192.214 124.836 1.00259.19 ATOM 207 CA HIS C 167 109.185 190.884 125.041 1.00259.19 ATOM 208 C HIS C 167 108.567 190.352 123.754 1.00259.19 ATOM 209 O HIS C 167 108.692 189.162 123.441 1.00259.19 ATOM 210 CB HIS C 167 108.146 190.916 126.163 1.00259.19 ATOM 211 CG HIS C 167 108.725 190.728 127.530 1.00259.19 ATOM 212 ND1 HIS C 167 109.311 189.547 127.934 1.00259.19 ATOM 213 CD2 HIS C 167 108.802 191.567 128.590 1.00259.19 ATOM 214 CE1 HIS C 167 109.727 189.669 129.182 1.00259.19 ATOM 215 NE2 HIS C 167 109.432 190.886 129.603 1.00259.19 ATOM 216 N SER C 168 107.894 191.218 123.001 1.00261.05 ATOM 217 CA SER C 168 107.332 190.816 121.720 1.00261.05 ATOM 218 C SER C 168 108.445 190.448 120.746 1.00261.05 ATOM 219 O SER C 168 109.494 191.095 120.700 1.00261.05 ATOM 220 CB SER C 168 106.476 191.943 121.142 1.00261.05 ATOM 221 OG SER C 168 105.343 192.191 121.958 1.00261.05 ATOM 222 N GLY C 169 108.211 189.397 119.966 1.00229.68 ATOM 223 CA GLY C 169 109.195 188.931 119.006 1.00229.68 ATOM 224 C GLY C 169 110.399 188.277 119.656 1.00229.68 ATOM 225 O GLY C 169 110.284 187.649 120.709 1.00229.68 ATOM 226 C1 8W7 C 502 105.627 190.471 138.522 1.00165.24 ATOM 227 C2 8W7 C 502 105.794 191.477 139.469 1.00165.24 ATOM 228 C3 8W7 C 502 106.977 191.545 140.197 1.00165.24 ATOM 229 C4 8W7 C 502 106.615 189.531 138.281 1.00165.24 ATOM 230 C5 8W7 C 502 107.784 189.615 139.014 1.00165.24 ATOM 231 C6 8W7 C 502 107.971 190.605 139.960 1.00165.24 ATOM 232 N1 8W7 C 502 109.708 189.128 140.088 1.00165.24 ATOM 233 N2 8W7 C 502 111.134 187.191 142.861 1.00165.24 ATOM 234 N3 8W7 C 502 100.769 190.777 143.396 1.00165.24 ATOM 235 O1 8W7 C 502 109.325 187.926 138.166 1.00165.24 ATOM 236 C7 8W7 C 502 109.320 190.443 140.589 1.00165.24 ATOM 237 C8 8W7 C 502 108.991 188.775 138.988 1.00165.24 ATOM 238 C9 8W7 C 502 110.720 188.284 140.706 1.00165.24 ATOM 239 C10 8W7 C 502 112.001 189.063 140.954 1.00165.24 ATOM 240 C11 8W7 C 502 113.026 188.166 141.641 1.00165.24 ATOM 241 C12 8W7 C 502 112.486 187.461 142.843 1.00165.24 ATOM 242 C13 8W7 C 502 110.185 187.682 141.996 1.00165.24 ATOM 243 C14 8W7 C 502 106.293 193.548 141.307 1.00165.24 ATOM 244 C15 8W7 C 502 105.108 193.020 142.061 1.00165.24 ATOM 245 O2 8W7 C 502 109.005 187.622 142.264 1.00165.24 ATOM 246 C22 8W7 C 502 100.545 189.426 143.899 1.00165.24 ATOM 247 C23 8W7 C 502 99.391 188.780 143.178 1.00165.24 ATOM 248 O5 8W7 C 502 99.046 189.484 141.994 1.00165.24 ATOM 249 C24 8W7 C 502 98.582 190.784 142.327 1.00165.24 ATOM 250 C25 8W7 C 502 99.485 191.466 143.322 1.00165.24 ATOM 251 C21 8W7 C 502 101.717 191.506 144.235 1.00165.24 ATOM 252 C20 8W7 C 502 102.905 192.037 143.472 1.00165.24 ATOM 253 C19 8W7 C 502 104.154 192.088 144.062 1.00165.24 ATOM 254 C17 8W7 C 502 105.246 192.573 143.364 1.00165.24 ATOM 255 C18 8W7 C 502 102.767 192.481 142.169 1.00165.24 ATOM 256 C16 8W7 C 502 103.858 192.966 141.469 1.00165.24 ATOM 257 O4 8W7 C 502 107.246 192.492 141.151 1.00165.24 ATOM 258 O3 8W7 C 502 113.189 187.119 143.774 1.00165.24 ATOM 259 ZN ZN C 201 109.218 192.237 131.111 1.00299.91 TER