HEADER HYDROLASE/HYDROLASE INHIBITOR 31-DEC-69 7E35 TITLE Crystal structure of the SARS-CoV-2 papain-like protease (PLPro) TITLE 2 C112S mutant bound to compound S43 COMPND MOL_ID: 1; COMPND 2 MOLECULE: Non-structural protein 3; COMPND 3 CHAIN: B, A; COMPND 4 MUTATION: YES; COMPND 5 EC: 3.4.19.121,3.4.22.-; COMPND 6 FRAGMENT: papain-like protease ; COMPND 7 ENGINEERED: YES; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 2.40 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 VAL B 20 REMARK 465 VAL B 21 REMARK 465 ASP B 22 REMARK 465 MET B 23 REMARK 465 SER B 24 REMARK 465 MET B 25 REMARK 465 THR B 26 REMARK 465 TYR B 27 REMARK 465 GLY B 28 REMARK 465 GLN B 29 REMARK 465 GLN B 30 REMARK 465 THR B 54 REMARK 465 PHE B 55 REMARK 465 TYR B 56 REMARK 465 VAL B 57 DBREF 7E35 B 2 316 UNP P0DTD1 R1AB_SARS2 1564 1878 SEQRES 1 B 52 THR THR VAL ASP ASN ILE ASN LEU HIS THR GLN VAL VAL SEQRES 2 B 52 ASP MET SER MET THR TYR GLY GLN GLN PHE GLY PRO THR SEQRES 3 B 52 TYR LEU ASP GLY ALA ASP VAL THR LYS ILE LYS PRO HIS SEQRES 4 B 52 ASN SER HIS GLU GLY LYS THR PHE TYR VAL LEU PRO ASN ATOM 1 N THR B 10 -46.556 -15.245 25.455 1.00182.37 ATOM 2 CA THR B 10 -45.677 -15.146 24.279 1.00178.59 ATOM 3 C THR B 10 -44.314 -15.778 24.539 1.00175.94 ATOM 4 O THR B 10 -43.903 -15.943 25.685 1.00178.46 ATOM 5 CB THR B 10 -45.429 -13.672 23.844 1.00181.08 ATOM 6 OG1 THR B 10 -44.897 -12.909 24.942 1.00180.37 ATOM 7 CG2 THR B 10 -46.706 -13.018 23.353 1.00181.26 ATOM 8 N THR B 11 -43.606 -16.116 23.454 1.00150.90 ATOM 9 CA THR B 11 -42.353 -16.837 23.618 1.00132.93 ATOM 10 C THR B 11 -41.466 -16.754 22.376 1.00119.19 ATOM 11 O THR B 11 -41.932 -16.549 21.245 1.00111.14 ATOM 12 CB THR B 11 -42.663 -18.305 23.954 1.00131.54 ATOM 13 OG1 THR B 11 -41.472 -18.958 24.444 1.00127.53 ATOM 14 CG2 THR B 11 -43.360 -19.070 22.753 1.00121.65 ATOM 15 N VAL B 12 -40.168 -16.935 22.627 1.00115.81 ATOM 16 CA VAL B 12 -39.187 -17.288 21.608 1.00109.08 ATOM 17 C VAL B 12 -38.559 -18.658 21.849 1.00109.36 ATOM 18 O VAL B 12 -37.940 -19.201 20.924 1.00102.94 ATOM 19 CB VAL B 12 -38.080 -16.207 21.497 1.00 93.11 ATOM 20 CG1 VAL B 12 -38.661 -14.910 20.968 1.00 94.06 ATOM 21 CG2 VAL B 12 -37.387 -15.982 22.853 1.00 96.79 ATOM 22 N ASP B 13 -38.695 -19.257 23.053 1.00113.98 ATOM 23 CA ASP B 13 -38.043 -20.539 23.322 1.00107.33 ATOM 24 C ASP B 13 -38.942 -21.657 23.829 1.00112.61 ATOM 25 O ASP B 13 -38.443 -22.766 24.063 1.00111.08 ATOM 26 CB ASP B 13 -36.922 -20.349 24.356 1.00104.92 ATOM 27 N ASN B 14 -40.231 -21.405 24.018 1.00128.53 ATOM 28 CA ASN B 14 -41.190 -22.378 24.538 1.00117.15 ATOM 29 C ASN B 14 -40.834 -22.787 25.967 1.00121.29 ATOM 30 O ASN B 14 -41.298 -23.821 26.456 1.00110.08 ATOM 31 CB ASN B 14 -41.302 -23.613 23.636 1.00 96.73 ATOM 32 N ILE B 15 -39.971 -22.008 26.633 1.00115.49 ATOM 33 CA ILE B 15 -39.628 -22.246 28.032 1.00116.50 ATOM 34 C ILE B 15 -39.929 -20.990 28.834 1.00120.45 ATOM 35 O ILE B 15 -40.759 -21.005 29.751 1.00124.31 ATOM 36 CB ILE B 15 -38.156 -22.673 28.208 1.00116.10 ATOM 37 CG1 ILE B 15 -37.893 -24.004 27.497 1.00109.87 ATOM 38 CG2 ILE B 15 -37.770 -22.715 29.695 1.00115.06 ATOM 39 CD1 ILE B 15 -38.410 -25.197 28.263 1.00107.87 ATOM 40 N ASN B 16 -39.258 -19.890 28.505 1.00124.64 ATOM 41 CA ASN B 16 -39.564 -18.636 29.174 1.00128.09 ATOM 42 C ASN B 16 -40.792 -18.015 28.528 1.00135.15 ATOM 43 O ASN B 16 -40.776 -17.746 27.322 1.00139.67 ATOM 44 CB ASN B 16 -38.372 -17.680 29.097 1.00122.81 ATOM 45 N LEU B 17 -41.869 -17.824 29.290 1.00131.96 ATOM 46 CA LEU B 17 -43.068 -17.256 28.693 1.00139.14 ATOM 47 C LEU B 17 -43.245 -15.825 29.184 1.00157.60 ATOM 48 O LEU B 17 -42.894 -15.493 30.323 1.00159.20 ATOM 49 CB LEU B 17 -44.313 -18.083 28.991 1.00129.80 ATOM 50 CG LEU B 17 -44.140 -19.546 28.611 1.00126.48 ATOM 51 CD1 LEU B 17 -43.912 -20.414 29.842 1.00125.50 ATOM 52 CD2 LEU B 17 -45.352 -19.989 27.829 1.00124.91 ATOM 53 N HIS B 18 -43.825 -14.989 28.320 1.00164.80 ATOM 54 CA HIS B 18 -44.077 -13.579 28.608 1.00164.17 ATOM 55 C HIS B 18 -45.535 -13.264 28.293 1.00165.19 ATOM 56 O HIS B 18 -45.951 -13.361 27.134 1.00168.01 ATOM 57 CB HIS B 18 -43.103 -12.693 27.822 1.00158.93 ATOM 58 CG HIS B 18 -41.669 -13.019 28.106 1.00156.46 ATOM 59 ND1 HIS B 18 -41.226 -13.358 29.368 1.00154.88 ATOM 60 CD2 HIS B 18 -40.588 -13.097 27.295 1.00155.01 ATOM 61 CE1 HIS B 18 -39.931 -13.614 29.325 1.00157.05 ATOM 62 NE2 HIS B 18 -39.518 -13.463 28.079 1.00157.03 ATOM 63 N THR B 19 -46.316 -12.911 29.313 1.00163.82 ATOM 64 CA THR B 19 -47.739 -12.649 29.106 1.00158.28 ATOM 65 C THR B 19 -47.972 -11.398 28.252 1.00159.62 ATOM 66 O THR B 19 -47.340 -10.353 28.459 1.00158.46 ATOM 67 CB THR B 19 -48.439 -12.500 30.453 1.00164.17 ATOM 68 OG1 THR B 19 -48.091 -11.237 31.036 1.00168.25 ATOM 69 CG2 THR B 19 -48.003 -13.619 31.398 1.00164.26 ATOM 70 N GLN B 20 -48.867 -11.517 27.274 1.00162.93 ATOM 71 CA GLN B 20 -49.257 -10.374 26.452 1.00146.07 ATOM 72 C GLN B 20 -50.777 -10.363 26.314 1.00117.64 ATOM 73 O GLN B 20 -51.398 -11.424 26.253 1.00105.59 ATOM 74 CB GLN B 20 -48.573 -10.407 25.084 1.00141.56 ATOM 75 N PHE B 32 -47.998 -7.588 17.365 1.00116.31 ATOM 76 CA PHE B 32 -47.053 -8.364 18.171 1.00122.64 ATOM 77 C PHE B 32 -45.614 -8.327 17.613 1.00129.80 ATOM 78 O PHE B 32 -44.649 -8.698 18.293 1.00126.71 ATOM 79 CB PHE B 32 -47.529 -9.810 18.284 1.00112.67 ATOM 80 N GLY B 33 -45.481 -7.871 16.374 1.00126.55 ATOM 81 CA GLY B 33 -44.310 -8.132 15.574 1.00127.22 ATOM 82 C GLY B 33 -44.375 -9.489 14.901 1.00132.45 ATOM 83 O GLY B 33 -45.454 -10.071 14.722 1.00135.94 ATOM 84 N PRO B 34 -43.224 -9.976 14.434 1.00142.17 ATOM 85 CA PRO B 34 -43.185 -11.288 13.769 1.00142.17 ATOM 86 C PRO B 34 -43.734 -12.404 14.653 1.00138.77 ATOM 87 O PRO B 34 -43.356 -12.532 15.823 1.00136.95 ATOM 88 CB PRO B 34 -41.694 -11.480 13.464 1.00142.22 ATOM 89 CG PRO B 34 -41.148 -10.070 13.363 1.00137.79 ATOM 90 CD PRO B 34 -41.923 -9.284 14.393 1.00138.77 ATOM 91 N THR B 35 -44.645 -13.205 14.089 1.00140.92 ATOM 92 CA THR B 35 -45.396 -14.191 14.862 1.00139.27 ATOM 93 C THR B 35 -45.529 -15.506 14.088 1.00141.35 ATOM 94 O THR B 35 -45.744 -15.493 12.871 1.00144.30 ATOM 95 CB THR B 35 -46.790 -13.639 15.251 1.00132.72 ATOM 96 OG1 THR B 35 -47.442 -13.051 14.114 1.00133.15 ATOM 97 CG2 THR B 35 -46.649 -12.579 16.333 1.00123.83 ATOM 98 N TYR B 36 -45.393 -16.646 14.777 1.00134.08 ATOM 99 CA TYR B 36 -45.451 -17.942 14.106 1.00129.65 ATOM 100 C TYR B 36 -46.366 -18.874 14.892 1.00139.80 ATOM 101 O TYR B 36 -46.389 -18.829 16.127 1.00142.42 ATOM 102 CB TYR B 36 -44.054 -18.567 13.960 1.00124.03 ATOM 103 N LEU B 37 -47.139 -19.704 14.173 1.00138.70 ATOM 104 CA LEU B 37 -48.025 -20.717 14.765 1.00137.17 ATOM 105 C LEU B 37 -47.693 -22.133 14.277 1.00137.14 ATOM 106 O LEU B 37 -48.071 -22.505 13.161 1.00137.22 ATOM 107 CB LEU B 37 -49.496 -20.400 14.474 1.00137.16 ATOM 108 CG LEU B 37 -50.479 -21.443 15.038 1.00135.04 ATOM 109 CD1 LEU B 37 -50.331 -21.559 16.557 1.00133.84 ATOM 110 CD2 LEU B 37 -51.935 -21.210 14.621 1.00130.90 ATOM 111 N ASP B 38 -47.003 -22.925 15.100 1.00138.22 ATOM 112 CA ASP B 38 -46.621 -24.316 14.778 1.00134.54 ATOM 113 C ASP B 38 -45.888 -24.482 13.433 1.00133.72 ATOM 114 O ASP B 38 -46.115 -25.448 12.696 1.00127.02 ATOM 115 CB ASP B 38 -47.852 -25.231 14.839 1.00123.42 ATOM 116 N GLY B 39 -44.967 -23.553 13.130 1.00140.75 ATOM 117 CA GLY B 39 -44.115 -23.555 11.938 1.00131.58 ATOM 118 C GLY B 39 -44.574 -22.722 10.747 1.00132.99 ATOM 119 O GLY B 39 -43.731 -22.309 9.940 1.00132.04 ATOM 120 N ALA B 40 -45.874 -22.471 10.611 1.00139.27 ATOM 121 CA ALA B 40 -46.410 -21.699 9.492 1.00132.07 ATOM 122 C ALA B 40 -46.229 -20.211 9.749 1.00131.26 ATOM 123 O ALA B 40 -46.533 -19.732 10.843 1.00136.49 ATOM 124 CB ALA B 40 -47.882 -22.039 9.260 1.00136.15 ATOM 125 N ASP B 41 -45.754 -19.459 8.759 1.00133.68 ATOM 126 CA ASP B 41 -45.583 -18.035 9.032 1.00137.75 ATOM 127 C ASP B 41 -46.967 -17.392 8.995 1.00139.47 ATOM 128 O ASP B 41 -47.596 -17.286 7.933 1.00134.72 ATOM 129 CB ASP B 41 -44.633 -17.383 8.024 1.00128.52 ATOM 130 N VAL B 42 -47.455 -17.011 10.175 1.00138.52 ATOM 131 CA VAL B 42 -48.746 -16.363 10.325 1.00141.12 ATOM 132 C VAL B 42 -48.613 -14.882 10.699 1.00146.91 ATOM 133 O VAL B 42 -49.579 -14.284 11.171 1.00147.65 ATOM 134 CB VAL B 42 -49.609 -17.120 11.343 1.00142.92 ATOM 135 CG1 VAL B 42 -49.872 -18.541 10.852 1.00136.36 ATOM 136 CG2 VAL B 42 -48.904 -17.128 12.700 1.00141.59 ATOM 137 N THR B 43 -47.428 -14.277 10.540 1.00152.49 ATOM 138 CA THR B 43 -47.282 -12.872 10.932 1.00154.34 ATOM 139 C THR B 43 -48.331 -12.028 10.221 1.00161.99 ATOM 140 O THR B 43 -48.960 -11.150 10.829 1.00158.42 ATOM 141 CB THR B 43 -45.865 -12.336 10.655 1.00142.69 ATOM 142 OG1 THR B 43 -44.888 -13.162 11.298 1.00132.62 ATOM 143 CG2 THR B 43 -45.717 -10.912 11.207 1.00139.24 ATOM 144 N LYS B 44 -48.589 -12.354 8.949 1.00175.73 ATOM 145 CA LYS B 44 -49.471 -11.606 8.068 1.00178.20 ATOM 146 C LYS B 44 -50.857 -12.227 7.973 1.00180.41 ATOM 147 O LYS B 44 -51.584 -11.955 7.012 1.00185.40 ATOM 148 CB LYS B 44 -48.853 -11.494 6.670 1.00179.09 ATOM 149 N ILE B 45 -51.210 -13.104 8.909 1.00172.45 ATOM 150 CA ILE B 45 -52.515 -13.749 8.908 1.00168.23 ATOM 151 C ILE B 45 -53.272 -13.190 10.107 1.00168.09 ATOM 152 O ILE B 45 -52.676 -12.865 11.143 1.00167.07 ATOM 153 CB ILE B 45 -52.420 -15.289 8.963 1.00158.91 ATOM 154 N LYS B 46 -54.623 -13.042 9.956 1.00170.31 ATOM 155 CA LYS B 46 -55.304 -12.626 11.175 1.00169.53 ATOM 156 C LYS B 46 -55.875 -13.827 11.938 1.00172.54 ATOM 157 O LYS B 46 -56.241 -14.846 11.333 1.00171.65 ATOM 158 CB LYS B 46 -56.426 -11.633 10.845 1.00168.84 ATOM 159 N PRO B 47 -55.992 -13.719 13.267 1.00166.14 ATOM 160 CA PRO B 47 -56.401 -14.879 14.072 1.00150.68 ATOM 161 C PRO B 47 -57.738 -15.460 13.629 1.00149.16 ATOM 162 O PRO B 47 -58.691 -14.730 13.350 1.00149.38 ATOM 163 CB PRO B 47 -56.478 -14.311 15.494 1.00141.15 ATOM 164 CG PRO B 47 -55.519 -13.162 15.488 1.00137.43 ATOM 165 CD PRO B 47 -55.631 -12.562 14.114 1.00152.78 ATOM 166 N HIS B 48 -57.799 -16.786 13.571 1.00148.84 ATOM 167 CA HIS B 48 -59.047 -17.511 13.368 1.00143.17 ATOM 168 C HIS B 48 -59.605 -17.853 14.740 1.00148.71 ATOM 169 O HIS B 48 -58.883 -17.882 15.738 1.00153.71 ATOM 170 CB HIS B 48 -58.922 -18.780 12.516 1.00138.80 ATOM 171 CG HIS B 48 -60.254 -19.320 12.071 1.00145.88 ATOM 172 ND1 HIS B 48 -60.625 -20.639 12.237 1.00157.51 ATOM 173 CD2 HIS B 48 -61.319 -18.704 11.500 1.00145.75 ATOM 174 CE1 HIS B 48 -61.855 -20.814 11.781 1.00144.47 ATOM 175 NE2 HIS B 48 -62.300 -19.656 11.328 1.00142.14 ATOM 176 N ASN B 49 -60.913 -18.090 14.785 1.00156.12 ATOM 177 CA ASN B 49 -61.547 -18.451 16.047 1.00156.36 ATOM 178 C ASN B 49 -60.973 -19.739 16.625 1.00170.23 ATOM 179 O ASN B 49 -60.903 -19.872 17.852 1.00167.15 ATOM 180 CB ASN B 49 -63.058 -18.583 15.851 1.00141.48 ATOM 181 N SER B 50 -60.581 -20.706 15.790 1.00190.46 ATOM 182 CA SER B 50 -59.978 -21.904 16.373 1.00191.61 ATOM 183 C SER B 50 -58.633 -21.625 17.062 1.00187.77 ATOM 184 O SER B 50 -58.141 -22.497 17.786 1.00188.22 ATOM 185 CB SER B 50 -59.818 -22.985 15.290 1.00193.26 ATOM 186 OG SER B 50 -58.835 -22.637 14.325 1.00189.21 ATOM 187 N HIS B 51 -58.024 -20.451 16.839 1.00170.95 ATOM 188 CA HIS B 51 -56.755 -20.024 17.435 1.00161.66 ATOM 189 C HIS B 51 -56.851 -19.532 18.888 1.00161.06 ATOM 190 O HIS B 51 -55.809 -19.405 19.540 1.00157.39 ATOM 191 CB HIS B 51 -56.114 -18.930 16.574 1.00150.60 ATOM 192 N GLU B 52 -58.055 -19.256 19.406 1.00159.85 ATOM 193 CA GLU B 52 -58.252 -18.664 20.740 1.00157.34 ATOM 194 C GLU B 52 -57.621 -19.412 21.914 1.00155.19 ATOM 195 O GLU B 52 -57.805 -20.621 22.086 1.00150.44 ATOM 196 CB GLU B 52 -59.750 -18.493 21.030 1.00149.22 ATOM 197 CG GLU B 52 -60.047 -17.905 22.425 1.00141.82 ATOM 198 CD GLU B 52 -60.188 -16.396 22.430 1.00140.10 ATOM 199 N GLY B 53 -56.884 -18.653 22.735 1.00159.79 ATOM 200 CA GLY B 53 -56.203 -19.109 23.932 1.00152.33 ATOM 201 C GLY B 53 -54.853 -19.779 23.785 1.00151.98 ATOM 202 O GLY B 53 -54.241 -20.097 24.812 1.00149.72 ATOM 203 N LYS B 54 -54.356 -20.005 22.573 1.00155.18 ATOM 204 CA LYS B 54 -53.071 -20.696 22.421 1.00142.54 ATOM 205 C LYS B 54 -51.891 -19.721 22.525 1.00135.82 ATOM 206 O LYS B 54 -51.617 -19.152 23.588 1.00130.66 ATOM 207 CB LYS B 54 -53.017 -21.454 21.090 1.00129.98 ATOM 208 N LEU B 59 -40.721 -12.018 16.582 1.00119.53 ATOM 209 CA LEU B 59 -39.260 -12.052 16.670 1.00118.99 ATOM 210 C LEU B 59 -38.795 -11.372 17.950 1.00120.34 ATOM 211 O LEU B 59 -39.483 -10.484 18.457 1.00126.43 ATOM 212 CB LEU B 59 -38.614 -11.374 15.457 1.00116.24 ATOM 213 N PRO B 60 -37.600 -11.759 18.451 1.00113.43 ATOM 214 CA PRO B 60 -37.085 -11.149 19.691 1.00115.91 ATOM 215 C PRO B 60 -36.702 -9.682 19.545 1.00130.10 ATOM 216 O PRO B 60 -35.591 -9.333 19.136 1.00131.09 ATOM 217 CB PRO B 60 -35.863 -12.017 20.036 1.00103.87 ATOM 218 CG PRO B 60 -36.033 -13.279 19.228 1.00 98.13 ATOM 219 CD PRO B 60 -36.733 -12.852 17.978 1.00102.62 ATOM 220 N ASN B 61 -37.653 -8.820 19.906 1.00142.83 ATOM 221 CA ASN B 61 -37.621 -7.374 19.688 1.00146.32 ATOM 222 C ASN B 61 -37.609 -6.586 21.003 1.00147.09 ATOM 223 O ASN B 61 -37.662 -5.348 20.982 1.00147.50 ATOM 224 CB ASN B 61 -38.781 -6.945 18.771 1.00142.88 ATOM 225 CG ASN B 61 -40.150 -7.286 19.340 1.00140.89 ATOM 226 OD1 ASN B 61 -40.520 -6.850 20.436 1.00140.18 ATOM 227 ND2 ASN B 61 -40.921 -8.060 18.575 1.00140.14 TER