HEADER VIRAL PROTEIN/INHIBITOR 20-JUN-13 4LAJ TITLE Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex TITLE 2 with CD4-mimetic miniprotein, M48U1, and llama single-domain, broadly TITLE 3 neutralizing, co-receptor binding site antibody, JM4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 YU2 gp120 envelope glycoprotein; COMPND 3 CHAIN: J, F, A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 CD4-mimetic miniprotein M48U1; COMPND 7 CHAIN: K, D, G, C; COMPND 8 ENGINEERED: YES; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 2.14 ANGSTORMS DBREF 4LAJ A 20 492 PDB 4LAJ 4LAJ 20 492 DBREF 4LAJ D 1 28 PDB 4LAJ 4LAJ 1 28 MODRES 4LAJ U2X D 23 TYR O-(CYCLOHEXYLMETHYL)-L-TYROSINE SEQRES 1 D 28 MPT ASN LEU HIS PHE CYS GLN LEU ARG CYS LYS SER LEU SEQRES 2 D 28 GLY LEU LEU GLY ARG CYS ALA DPR THR TYR CYS ALA CYS SEQRES 3 D 28 VAL NH2 ATOM 1 C1 EDO A 510 3.661 0.309 -65.520 1.00 64.85 ATOM 2 O1 EDO A 510 3.875 0.728 -66.869 1.00 66.27 ATOM 3 C2 EDO A 510 2.401 -0.544 -65.431 1.00 63.55 ATOM 4 O2 EDO A 510 1.797 -0.648 -66.718 1.00 62.52 TER ATOM 1 CA MPT D 1 0.687 -13.457 -66.573 1.00 39.94 ATOM 2 C MPT D 1 1.582 -14.649 -66.554 1.00 43.71 ATOM 3 O MPT D 1 1.745 -15.308 -67.615 1.00 50.04 ATOM 4 CB MPT D 1 -0.772 -13.668 -66.341 1.00 48.25 ATOM 5 SG MPT D 1 -1.323 -15.308 -65.984 1.00 51.66 ATOM 6 N ASN D 2 2.603 -14.914 -65.618 1.00 50.13 ATOM 7 CA ASN D 2 2.990 -16.270 -65.982 1.00 55.37 ATOM 8 C ASN D 2 2.068 -17.293 -65.314 1.00 55.36 ATOM 9 O ASN D 2 1.907 -17.312 -64.090 1.00 48.45 ATOM 10 CB ASN D 2 4.463 -16.530 -65.641 1.00 72.42 ATOM 11 CG ASN D 2 4.717 -16.636 -64.155 1.00 75.98 ATOM 12 OD1 ASN D 2 5.155 -17.681 -63.665 1.00 80.94 ATOM 13 ND2 ASN D 2 4.454 -15.557 -63.428 1.00 65.20 ATOM 14 N LEU D 3 1.455 -18.136 -66.138 1.00 48.50 ATOM 15 CA LEU D 3 0.328 -18.954 -65.710 1.00 50.25 ATOM 16 C LEU D 3 0.680 -19.890 -64.557 1.00 51.54 ATOM 17 O LEU D 3 -0.099 -20.034 -63.616 1.00 57.75 ATOM 18 CB LEU D 3 -0.211 -19.765 -66.891 1.00 46.20 ATOM 19 CG LEU D 3 -1.536 -20.494 -66.660 1.00 50.11 ATOM 20 CD1 LEU D 3 -2.581 -19.518 -66.139 1.00 45.90 ATOM 21 CD2 LEU D 3 -2.018 -21.188 -67.930 1.00 55.18 ATOM 22 N HIS D 4 1.842 -20.527 -64.633 1.00 55.56 ATOM 23 CA HIS D 4 2.238 -21.506 -63.624 1.00 63.01 ATOM 24 C HIS D 4 2.298 -20.903 -62.220 1.00 62.69 ATOM 25 O HIS D 4 1.780 -21.487 -61.267 1.00 67.24 ATOM 26 CB HIS D 4 3.588 -22.128 -63.985 1.00 68.50 ATOM 27 CG HIS D 4 4.078 -23.130 -62.985 1.00 73.21 ATOM 28 ND1 HIS D 4 3.361 -24.257 -62.653 1.00 78.15 ATOM 29 CD2 HIS D 4 5.219 -23.180 -62.256 1.00 73.57 ATOM 30 CE1 HIS D 4 4.034 -24.958 -61.756 1.00 79.10 ATOM 31 NE2 HIS D 4 5.164 -24.326 -61.499 1.00 77.95 ATOM 32 N PHE D 5 2.926 -19.738 -62.092 1.00 55.26 ATOM 33 CA PHE D 5 3.036 -19.089 -60.791 1.00 57.32 ATOM 34 C PHE D 5 1.671 -18.596 -60.316 1.00 54.99 ATOM 35 O PHE D 5 1.367 -18.622 -59.123 1.00 54.49 ATOM 36 CB PHE D 5 4.032 -17.931 -60.846 1.00 69.48 ATOM 37 CG PHE D 5 4.222 -17.232 -59.529 1.00 85.62 ATOM 38 CD1 PHE D 5 4.836 -17.879 -58.466 1.00 92.67 ATOM 39 CD2 PHE D 5 3.792 -15.925 -59.353 1.00 88.48 ATOM 40 CE1 PHE D 5 5.012 -17.236 -57.250 1.00 94.04 ATOM 41 CE2 PHE D 5 3.968 -15.276 -58.143 1.00 88.32 ATOM 42 CZ PHE D 5 4.576 -15.933 -57.089 1.00 89.79 ATOM 43 N CYS D 6 0.846 -18.154 -61.259 1.00 46.52 ATOM 44 CA CYS D 6 -0.484 -17.674 -60.934 1.00 47.31 ATOM 45 C CYS D 6 -1.358 -18.808 -60.397 1.00 50.27 ATOM 46 O CYS D 6 -2.064 -18.646 -59.403 1.00 49.12 ATOM 47 CB CYS D 6 -1.135 -17.040 -62.162 1.00 41.25 ATOM 48 SG CYS D 6 -2.858 -16.581 -61.907 1.00 54.59 ATOM 49 N GLN D 7 -1.305 -19.956 -61.060 1.00 49.35 ATOM 50 CA GLN D 7 -2.105 -21.101 -60.651 1.00 50.62 ATOM 51 C GLN D 7 -1.629 -21.636 -59.303 1.00 52.01 ATOM 52 O GLN D 7 -2.430 -22.105 -58.498 1.00 54.21 ATOM 53 CB GLN D 7 -2.072 -22.187 -61.727 1.00 51.33 ATOM 54 CG GLN D 7 -2.799 -21.757 -62.995 1.00 58.28 ATOM 55 CD GLN D 7 -2.858 -22.839 -64.052 1.00 60.73 ATOM 56 OE1 GLN D 7 -1.981 -23.698 -64.131 1.00 58.98 ATOM 57 NE2 GLN D 7 -3.899 -22.799 -64.878 1.00 66.65 ATOM 58 N LEU D 8 -0.325 -21.556 -59.059 1.00 52.67 ATOM 59 CA LEU D 8 0.230 -21.909 -57.757 1.00 54.58 ATOM 60 C LEU D 8 -0.310 -20.975 -56.674 1.00 54.63 ATOM 61 O LEU D 8 -0.761 -21.428 -55.622 1.00 59.57 ATOM 62 CB LEU D 8 1.759 -21.853 -57.788 1.00 59.40 ATOM 63 CG LEU D 8 2.507 -23.181 -57.918 1.00 67.31 ATOM 64 CD1 LEU D 8 2.042 -23.938 -59.152 1.00 75.33 ATOM 65 CD2 LEU D 8 4.014 -22.956 -57.963 1.00 65.93 ATOM 66 N ARG D 9 -0.262 -19.672 -56.940 1.00 52.86 ATOM 67 CA ARG D 9 -0.715 -18.664 -55.981 1.00 54.66 ATOM 68 C ARG D 9 -2.194 -18.790 -55.640 1.00 56.22 ATOM 69 O ARG D 9 -2.574 -18.759 -54.471 1.00 63.28 ATOM 70 CB ARG D 9 -0.451 -17.255 -56.506 1.00 54.39 ATOM 71 CG ARG D 9 0.984 -16.785 -56.392 1.00 69.41 ATOM 72 CD ARG D 9 1.107 -15.389 -56.978 1.00 81.06 ATOM 73 NE ARG D 9 0.130 -14.474 -56.389 1.00 88.46 ATOM 74 CZ ARG D 9 -0.304 -13.364 -56.977 1.00 85.07 ATOM 75 NH1 ARG D 9 0.149 -13.032 -58.178 1.00 87.63 ATOM 76 NH2 ARG D 9 -1.196 -12.591 -56.370 1.00 77.31 ATOM 77 N CYS D 10 -3.028 -18.911 -56.667 1.00 52.84 ATOM 78 CA CYS D 10 -4.465 -18.999 -56.458 1.00 53.07 ATOM 79 C CYS D 10 -4.811 -20.303 -55.738 1.00 53.79 ATOM 80 O CYS D 10 -5.776 -20.353 -54.975 1.00 54.40 ATOM 81 CB CYS D 10 -5.214 -18.890 -57.788 1.00 39.23 ATOM 82 SG CYS D 10 -4.935 -17.334 -58.668 1.00 46.03 ATOM 83 N LYS D 11 -4.021 -21.350 -55.975 1.00 53.47 ATOM 84 CA LYS D 11 -4.188 -22.612 -55.251 1.00 55.47 ATOM 85 C LYS D 11 -4.138 -22.442 -53.739 1.00 66.02 ATOM 86 O LYS D 11 -4.894 -23.089 -53.012 1.00 67.72 ATOM 87 CB LYS D 11 -3.121 -23.628 -55.657 1.00 54.86 ATOM 88 CG LYS D 11 -3.512 -25.053 -55.312 1.00 61.72 ATOM 89 CD LYS D 11 -2.556 -26.083 -55.883 1.00 73.42 ATOM 90 CE LYS D 11 -2.361 -27.234 -54.896 1.00 82.78 ATOM 91 NZ LYS D 11 -3.637 -27.664 -54.251 1.00 84.45 ATOM 92 N SER D 12 -3.244 -21.579 -53.267 1.00 68.94 ATOM 93 CA SER D 12 -3.111 -21.345 -51.837 1.00 72.02 ATOM 94 C SER D 12 -4.386 -20.706 -51.296 1.00 70.98 ATOM 95 O SER D 12 -4.665 -20.768 -50.099 1.00 75.20 ATOM 96 CB SER D 12 -1.897 -20.467 -51.543 1.00 74.38 ATOM 97 OG SER D 12 -2.160 -19.119 -51.882 1.00 84.78 ATOM 98 N LEU D 13 -5.163 -20.100 -52.188 1.00 67.34 ATOM 99 CA LEU D 13 -6.430 -19.489 -51.806 1.00 58.67 ATOM 100 C LEU D 13 -7.600 -20.430 -52.080 1.00 64.08 ATOM 101 O LEU D 13 -8.753 -20.090 -51.814 1.00 67.55 ATOM 102 CB LEU D 13 -6.637 -18.169 -52.551 1.00 60.11 ATOM 103 CG LEU D 13 -5.581 -17.072 -52.376 1.00 61.94 ATOM 104 CD1 LEU D 13 -5.990 -15.821 -53.136 1.00 60.37 ATOM 105 CD2 LEU D 13 -5.360 -16.754 -50.905 1.00 60.41 ATOM 106 N GLY D 14 -7.303 -21.614 -52.608 1.00 58.14 ATOM 107 CA GLY D 14 -8.337 -22.582 -52.923 1.00 52.72 ATOM 108 C GLY D 14 -9.025 -22.281 -54.240 1.00 51.54 ATOM 109 O GLY D 14 -10.127 -22.764 -54.501 1.00 49.99 ATOM 110 N LEU D 15 -8.369 -21.484 -55.077 1.00 44.60 ATOM 111 CA LEU D 15 -8.966 -21.034 -56.330 1.00 43.04 ATOM 112 C LEU D 15 -8.161 -21.443 -57.561 1.00 47.31 ATOM 113 O LEU D 15 -6.972 -21.750 -57.473 1.00 42.64 ATOM 114 CB LEU D 15 -9.133 -19.513 -56.321 1.00 39.77 ATOM 115 CG LEU D 15 -9.874 -18.899 -55.134 1.00 44.59 ATOM 116 CD1 LEU D 15 -9.996 -17.396 -55.314 1.00 43.71 ATOM 117 CD2 LEU D 15 -11.241 -19.546 -54.972 1.00 46.23 ATOM 118 N LEU D 16 -8.830 -21.441 -58.709 1.00 49.80 ATOM 119 CA LEU D 16 -8.164 -21.626 -59.987 1.00 47.02 ATOM 120 C LEU D 16 -7.420 -20.356 -60.362 1.00 50.25 ATOM 121 O LEU D 16 -7.807 -19.259 -59.964 1.00 44.87 ATOM 122 CB LEU D 16 -9.171 -21.979 -61.084 1.00 50.07 ATOM 123 CG LEU D 16 -10.161 -23.121 -60.849 1.00 51.98 ATOM 124 CD1 LEU D 16 -11.199 -23.156 -61.962 1.00 53.85 ATOM 125 CD2 LEU D 16 -9.437 -24.449 -60.757 1.00 51.00 ATOM 126 N GLY D 17 -6.346 -20.507 -61.124 1.00 51.17 ATOM 127 CA GLY D 17 -5.622 -19.360 -61.639 1.00 47.01 ATOM 128 C GLY D 17 -5.740 -19.306 -63.148 1.00 47.87 ATOM 129 O GLY D 17 -5.620 -20.328 -63.824 1.00 52.93 ATOM 130 N ARG D 18 -5.986 -18.117 -63.679 1.00 41.97 ATOM 131 CA ARG D 18 -5.934 -17.916 -65.116 1.00 42.64 ATOM 132 C ARG D 18 -5.397 -16.531 -65.423 1.00 48.78 ATOM 133 O ARG D 18 -5.389 -15.651 -64.567 1.00 48.53 ATOM 134 CB ARG D 18 -7.312 -18.091 -65.751 1.00 49.08 ATOM 135 CG ARG D 18 -8.304 -17.003 -65.396 1.00 53.64 ATOM 136 CD ARG D 18 -9.525 -17.073 -66.305 1.00 65.65 ATOM 137 NE ARG D 18 -10.684 -16.390 -65.735 1.00 72.93 ATOM 138 CZ ARG D 18 -11.943 -16.786 -65.900 1.00 79.79 ATOM 139 NH1 ARG D 18 -12.214 -17.867 -66.620 1.00 82.54 ATOM 140 NH2 ARG D 18 -12.934 -16.102 -65.344 1.00 79.69 ATOM 141 N CYS D 19 -4.931 -16.336 -66.646 1.00 44.03 ATOM 142 CA CYS D 19 -4.439 -15.030 -67.031 1.00 40.39 ATOM 143 C CYS D 19 -5.590 -14.095 -67.390 1.00 46.98 ATOM 144 O CYS D 19 -6.615 -14.517 -67.920 1.00 47.23 ATOM 145 CB CYS D 19 -3.473 -15.158 -68.207 1.00 39.30 ATOM 146 SG CYS D 19 -1.953 -16.060 -67.820 1.00 59.15 ATOM 147 N ALA D 20 -5.430 -12.629 -67.289 1.00 23.11 ATOM 148 CA ALA D 20 -6.250 -11.508 -67.718 1.00 21.13 ATOM 149 C ALA D 20 -5.261 -10.527 -68.321 1.00 19.11 ATOM 150 O ALA D 20 -4.724 -9.674 -67.625 1.00 21.03 ATOM 151 CB ALA D 20 -6.956 -10.890 -66.533 1.00 21.22 ATOM 152 N DPR D 21 -4.973 -10.682 -69.595 1.00 19.45 ATOM 153 CA DPR D 21 -3.872 -9.925 -70.191 1.00 19.58 ATOM 154 CB DPR D 21 -3.929 -10.325 -71.669 1.00 21.72 ATOM 155 CG DPR D 21 -4.545 -11.660 -71.663 1.00 24.95 ATOM 156 CD DPR D 21 -5.510 -11.692 -70.523 1.00 25.75 ATOM 157 C DPR D 21 -2.565 -10.345 -69.545 1.00 19.86 ATOM 158 O DPR D 21 -2.236 -11.532 -69.541 1.00 22.94 ATOM 159 N THR D 22 -1.881 -9.388 -68.956 1.00 20.34 ATOM 160 CA THR D 22 -0.594 -9.628 -68.314 1.00 19.04 ATOM 161 C THR D 22 -0.737 -9.887 -66.813 1.00 21.36 ATOM 162 O THR D 22 0.261 -10.038 -66.103 1.00 22.56 ATOM 163 CB THR D 22 0.318 -8.420 -68.479 1.00 20.02 ATOM 164 OG1 THR D 22 -0.310 -7.290 -67.867 1.00 20.69 ATOM 165 CG2 THR D 22 0.594 -8.129 -69.963 1.00 20.34 ATOM 166 N U2X D 23 -2.078 -10.018 -66.230 1.00 38.49 ATOM 167 C U2X D 23 -2.785 -11.575 -64.413 1.00 39.26 ATOM 168 O U2X D 23 -3.384 -12.311 -65.193 1.00 35.78 ATOM 169 CA U2X D 23 -2.350 -10.205 -64.833 1.00 39.81 ATOM 170 CB U2X D 23 -3.282 -9.193 -64.255 1.00 38.41 ATOM 171 CG U2X D 23 -3.063 -7.748 -64.568 1.00 41.37 ATOM 172 CD1 U2X D 23 -2.091 -7.016 -63.838 1.00 35.99 ATOM 173 CD2 U2X D 23 -3.834 -7.133 -65.549 1.00 40.38 ATOM 174 CE1 U2X D 23 -1.895 -5.595 -64.124 1.00 32.45 ATOM 175 CE2 U2X D 23 -3.634 -5.661 -65.847 1.00 35.47 ATOM 176 CZ U2X D 23 -2.693 -4.961 -65.138 1.00 33.66 ATOM 177 OH U2X D 23 -2.523 -3.614 -65.381 1.00 40.05 ATOM 178 C7 U2X D 23 -1.830 -2.845 -64.464 1.00 44.39 ATOM 179 C1 U2X D 23 -2.108 0.959 -63.855 1.00 47.25 ATOM 180 C2 U2X D 23 -1.588 -0.214 -64.645 1.00 47.84 ATOM 181 C3 U2X D 23 -2.395 -1.478 -64.199 1.00 39.76 ATOM 182 C4 U2X D 23 -3.946 -1.247 -64.440 1.00 45.07 ATOM 183 C5 U2X D 23 -4.371 0.065 -63.724 1.00 42.37 ATOM 184 C6 U2X D 23 -3.523 1.191 -64.247 1.00 42.94 ATOM 185 N CYS D 24 -2.518 -11.908 -63.173 1.00 35.97 ATOM 186 CA CYS D 24 -3.031 -13.135 -62.582 1.00 41.56 ATOM 187 C CYS D 24 -4.421 -12.925 -61.990 1.00 40.25 ATOM 188 O CYS D 24 -4.640 -12.023 -61.183 1.00 45.17 ATOM 189 CB CYS D 24 -2.089 -13.651 -61.498 1.00 34.94 ATOM 190 SG CYS D 24 -2.776 -15.043 -60.573 1.00 52.79 ATOM 191 N ALA D 25 -5.358 -13.768 -62.393 1.00 35.68 ATOM 192 CA ALA D 25 -6.698 -13.721 -61.838 1.00 39.41 ATOM 193 C ALA D 25 -7.012 -15.059 -61.202 1.00 43.82 ATOM 194 O ALA D 25 -6.730 -16.113 -61.778 1.00 45.32 ATOM 195 CB ALA D 25 -7.716 -13.380 -62.908 1.00 42.62 ATOM 196 N CYS D 26 -7.646 -15.024 -60.039 1.00 46.46 ATOM 197 CA CYS D 26 -8.108 -16.242 -59.386 1.00 47.75 ATOM 198 C CYS D 26 -9.587 -16.463 -59.670 1.00 53.21 ATOM 199 O CYS D 26 -10.392 -15.551 -59.553 1.00 52.27 ATOM 200 CB CYS D 26 -7.860 -16.184 -57.891 1.00 43.17 ATOM 201 SG CYS D 26 -6.127 -16.064 -57.444 1.00 56.36 ATOM 202 N VAL D 27 -9.926 -17.679 -60.068 1.00 43.98 ATOM 203 CA VAL D 27 -11.270 -18.018 -60.508 1.00 47.81 ATOM 204 C VAL D 27 -11.911 -19.022 -59.562 1.00 49.50 ATOM 205 O VAL D 27 -11.317 -20.044 -59.244 1.00 45.87 ATOM 206 CB VAL D 27 -11.279 -18.624 -61.917 1.00 51.77 ATOM 207 CG1 VAL D 27 -12.613 -18.373 -62.588 1.00 56.04 ATOM 208 CG2 VAL D 27 -10.148 -18.075 -62.757 1.00 58.83 ATOM 209 N NH2 D 28 -13.028 -18.436 -58.918 1.00 63.13 TER