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: 2; COMPND 2 MOLECULE: CD4-mimetic miniprotein M48U1; COMPND 3 CHAIN: K, D, G, C; COMPND 4 ENGINEERED: YES; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 2.14 ANGSTORMS DBREF 4LAJ G 1 28 PDB 4LAJ 4LAJ 1 28 MODRES 4LAJ U2X G 23 TYR O-(CYCLOHEXYLMETHYL)-L-TYROSINE SEQRES 1 G 28 MPT ASN LEU HIS PHE CYS GLN LEU ARG CYS LYS SER LEU SEQRES 2 G 28 GLY LEU LEU GLY ARG CYS ALA DPR THR TYR CYS ALA CYS SEQRES 3 G 28 VAL NH2 ATOM 1 CA MPT G 1 -38.846 6.603 -12.753 1.00 55.33 ATOM 2 C MPT G 1 -39.701 7.748 -12.332 1.00 57.61 ATOM 3 O MPT G 1 -40.596 8.171 -13.110 1.00 57.40 ATOM 4 CB MPT G 1 -37.515 6.905 -13.353 1.00 54.51 ATOM 5 SG MPT G 1 -37.314 8.433 -14.217 1.00 57.92 ATOM 6 N ASN G 2 -39.370 8.102 -11.028 1.00 63.40 ATOM 7 CA ASN G 2 -39.953 9.431 -10.899 1.00 63.56 ATOM 8 C ASN G 2 -39.049 10.497 -11.515 1.00 63.09 ATOM 9 O ASN G 2 -37.920 10.711 -11.064 1.00 63.40 ATOM 10 CB ASN G 2 -40.207 9.747 -9.427 1.00 73.11 ATOM 11 CG ASN G 2 -40.643 8.519 -8.636 1.00 81.96 ATOM 12 OD1 ASN G 2 -41.764 8.033 -8.799 1.00 81.87 ATOM 13 ND2 ASN G 2 -39.771 8.030 -7.761 1.00 82.00 ATOM 14 N LEU G 3 -39.554 11.176 -12.539 1.00 56.39 ATOM 15 CA LEU G 3 -38.701 12.023 -13.368 1.00 57.21 ATOM 16 C LEU G 3 -38.119 13.195 -12.593 1.00 61.33 ATOM 17 O LEU G 3 -36.929 13.480 -12.704 1.00 63.24 ATOM 18 CB LEU G 3 -39.462 12.533 -14.593 1.00 55.87 ATOM 19 CG LEU G 3 -38.555 13.259 -15.596 1.00 55.31 ATOM 20 CD1 LEU G 3 -37.332 12.421 -15.965 1.00 53.13 ATOM 21 CD2 LEU G 3 -39.332 13.638 -16.845 1.00 61.42 ATOM 22 N HIS G 4 -38.961 13.866 -11.811 1.00 63.92 ATOM 23 CA HIS G 4 -38.539 15.046 -11.063 1.00 66.58 ATOM 24 C HIS G 4 -37.392 14.691 -10.128 1.00 65.52 ATOM 25 O HIS G 4 -36.392 15.402 -10.055 1.00 69.87 ATOM 26 CB HIS G 4 -39.710 15.638 -10.278 1.00 70.07 ATOM 27 CG HIS G 4 -39.340 16.831 -9.450 1.00 76.76 ATOM 28 ND1 HIS G 4 -38.801 17.973 -9.994 1.00 80.06 ATOM 29 CD2 HIS G 4 -39.438 17.052 -8.117 1.00 79.01 ATOM 30 CE1 HIS G 4 -38.578 18.854 -9.030 1.00 80.72 ATOM 31 NE2 HIS G 4 -38.956 18.319 -7.886 1.00 81.80 ATOM 32 N PHE G 5 -37.539 13.573 -9.428 1.00 66.02 ATOM 33 CA PHE G 5 -36.519 13.111 -8.501 1.00 72.20 ATOM 34 C PHE G 5 -35.247 12.718 -9.237 1.00 70.02 ATOM 35 O PHE G 5 -34.141 12.967 -8.756 1.00 72.86 ATOM 36 CB PHE G 5 -37.052 11.923 -7.697 1.00 81.06 ATOM 37 CG PHE G 5 -36.056 11.335 -6.739 1.00 94.97 ATOM 38 CD1 PHE G 5 -35.626 12.040 -5.627 1.00102.30 ATOM 39 CD2 PHE G 5 -35.552 10.060 -6.957 1.00 98.62 ATOM 40 CE1 PHE G 5 -34.705 11.483 -4.752 1.00105.31 ATOM 41 CE2 PHE G 5 -34.635 9.499 -6.089 1.00100.45 ATOM 42 CZ PHE G 5 -34.210 10.209 -4.985 1.00103.29 ATOM 43 N CYS G 6 -35.410 12.127 -10.416 1.00 64.96 ATOM 44 CA CYS G 6 -34.277 11.712 -11.232 1.00 58.88 ATOM 45 C CYS G 6 -33.504 12.926 -11.732 1.00 60.75 ATOM 46 O CYS G 6 -32.273 12.954 -11.701 1.00 63.31 ATOM 47 CB CYS G 6 -34.743 10.859 -12.413 1.00 54.43 ATOM 48 SG CYS G 6 -33.429 10.439 -13.590 1.00 68.32 ATOM 49 N GLN G 7 -34.244 13.931 -12.189 1.00 57.00 ATOM 50 CA GLN G 7 -33.648 15.139 -12.742 1.00 58.37 ATOM 51 C GLN G 7 -32.898 15.938 -11.683 1.00 67.88 ATOM 52 O GLN G 7 -31.855 16.525 -11.966 1.00 69.29 ATOM 53 CB GLN G 7 -34.734 16.001 -13.385 1.00 56.85 ATOM 54 CG GLN G 7 -35.339 15.374 -14.628 1.00 63.12 ATOM 55 CD GLN G 7 -36.386 16.253 -15.280 1.00 72.35 ATOM 56 OE1 GLN G 7 -37.057 17.039 -14.610 1.00 77.42 ATOM 57 NE2 GLN G 7 -36.535 16.120 -16.593 1.00 73.86 ATOM 58 N LEU G 8 -33.427 15.952 -10.464 1.00 73.87 ATOM 59 CA LEU G 8 -32.735 16.570 -9.338 1.00 76.18 ATOM 60 C LEU G 8 -31.438 15.834 -9.030 1.00 71.74 ATOM 61 O LEU G 8 -30.382 16.450 -8.876 1.00 69.46 ATOM 62 CB LEU G 8 -33.626 16.591 -8.092 1.00 75.49 ATOM 63 CG LEU G 8 -34.317 17.908 -7.739 1.00 79.21 ATOM 64 CD1 LEU G 8 -35.158 18.409 -8.903 1.00 82.05 ATOM 65 CD2 LEU G 8 -35.164 17.745 -6.485 1.00 77.10 ATOM 66 N ARG G 9 -31.530 14.512 -8.943 1.00 64.24 ATOM 67 CA ARG G 9 -30.384 13.683 -8.599 1.00 71.43 ATOM 68 C ARG G 9 -29.272 13.828 -9.635 1.00 72.72 ATOM 69 O ARG G 9 -28.112 14.047 -9.285 1.00 78.83 ATOM 70 CB ARG G 9 -30.810 12.220 -8.463 1.00 74.35 ATOM 71 CG ARG G 9 -29.803 11.344 -7.738 1.00 82.08 ATOM 72 CD ARG G 9 -30.496 10.234 -6.961 1.00 87.26 ATOM 73 NE ARG G 9 -31.302 9.376 -7.825 1.00 92.88 ATOM 74 CZ ARG G 9 -30.806 8.388 -8.564 1.00 96.95 ATOM 75 NH1 ARG G 9 -29.503 8.138 -8.549 1.00 96.16 ATOM 76 NH2 ARG G 9 -31.610 7.654 -9.321 1.00 98.43 ATOM 77 N CYS G 10 -29.629 13.703 -10.908 1.00 68.04 ATOM 78 CA CYS G 10 -28.654 13.823 -11.984 1.00 66.39 ATOM 79 C CYS G 10 -28.138 15.254 -12.122 1.00 71.54 ATOM 80 O CYS G 10 -26.986 15.473 -12.496 1.00 76.36 ATOM 81 CB CYS G 10 -29.257 13.351 -13.306 1.00 59.34 ATOM 82 SG CYS G 10 -29.774 11.619 -13.293 1.00 54.77 ATOM 83 N LYS G 11 -28.999 16.223 -11.823 1.00 72.17 ATOM 84 CA LYS G 11 -28.612 17.632 -11.838 1.00 75.78 ATOM 85 C LYS G 11 -27.416 17.870 -10.922 1.00 75.72 ATOM 86 O LYS G 11 -26.514 18.636 -11.249 1.00 80.06 ATOM 87 CB LYS G 11 -29.789 18.516 -11.412 1.00 76.57 ATOM 88 CG LYS G 11 -30.119 19.652 -12.372 1.00 82.53 ATOM 89 CD LYS G 11 -31.434 20.320 -11.983 1.00 85.98 ATOM 90 CE LYS G 11 -31.423 21.818 -12.252 1.00 89.84 ATOM 91 NZ LYS G 11 -30.828 22.157 -13.576 1.00 93.07 ATOM 92 N SER G 12 -27.420 17.199 -9.774 1.00 78.36 ATOM 93 CA SER G 12 -26.350 17.328 -8.791 1.00 78.63 ATOM 94 C SER G 12 -25.013 16.780 -9.289 1.00 78.81 ATOM 95 O SER G 12 -23.954 17.157 -8.785 1.00 81.32 ATOM 96 CB SER G 12 -26.744 16.618 -7.496 1.00 74.71 ATOM 97 OG SER G 12 -26.638 15.214 -7.642 1.00 66.66 ATOM 98 N LEU G 13 -25.066 15.905 -10.289 1.00 73.72 ATOM 99 CA LEU G 13 -23.858 15.321 -10.866 1.00 72.28 ATOM 100 C LEU G 13 -23.428 16.092 -12.110 1.00 73.09 ATOM 101 O LEU G 13 -22.451 15.736 -12.769 1.00 78.24 ATOM 102 CB LEU G 13 -24.080 13.846 -11.208 1.00 73.45 ATOM 103 CG LEU G 13 -24.497 12.919 -10.064 1.00 79.11 ATOM 104 CD1 LEU G 13 -24.608 11.489 -10.557 1.00 80.34 ATOM 105 CD2 LEU G 13 -23.523 13.009 -8.898 1.00 82.32 ATOM 106 N GLY G 14 -24.170 17.147 -12.427 1.00 69.63 ATOM 107 CA GLY G 14 -23.888 17.961 -13.594 1.00 70.17 ATOM 108 C GLY G 14 -24.448 17.353 -14.863 1.00 68.76 ATOM 109 O GLY G 14 -24.028 17.700 -15.967 1.00 74.96 ATOM 110 N LEU G 15 -25.398 16.438 -14.702 1.00 62.23 ATOM 111 CA LEU G 15 -25.976 15.723 -15.833 1.00 63.04 ATOM 112 C LEU G 15 -27.487 15.923 -15.899 1.00 72.32 ATOM 113 O LEU G 15 -28.118 16.260 -14.899 1.00 76.79 ATOM 114 CB LEU G 15 -25.655 14.232 -15.735 1.00 55.00 ATOM 115 CG LEU G 15 -24.183 13.872 -15.541 1.00 56.21 ATOM 116 CD1 LEU G 15 -23.994 12.360 -15.502 1.00 50.84 ATOM 117 CD2 LEU G 15 -23.338 14.500 -16.639 1.00 56.10 ATOM 118 N LEU G 16 -28.066 15.727 -17.078 1.00 72.41 ATOM 119 CA LEU G 16 -29.516 15.673 -17.184 1.00 68.32 ATOM 120 C LEU G 16 -29.994 14.319 -16.702 1.00 66.95 ATOM 121 O LEU G 16 -29.266 13.326 -16.770 1.00 67.91 ATOM 122 CB LEU G 16 -30.001 15.929 -18.612 1.00 71.59 ATOM 123 CG LEU G 16 -29.510 17.185 -19.328 1.00 78.91 ATOM 124 CD1 LEU G 16 -29.942 17.157 -20.784 1.00 81.97 ATOM 125 CD2 LEU G 16 -30.031 18.434 -18.635 1.00 84.94 ATOM 126 N GLY G 17 -31.223 14.281 -16.210 1.00 58.57 ATOM 127 CA GLY G 17 -31.834 13.033 -15.816 1.00 56.80 ATOM 128 C GLY G 17 -32.985 12.723 -16.746 1.00 58.28 ATOM 129 O GLY G 17 -33.767 13.605 -17.097 1.00 62.07 ATOM 130 N ARG G 18 -33.077 11.468 -17.163 1.00 52.51 ATOM 131 CA ARG G 18 -34.240 11.004 -17.895 1.00 56.43 ATOM 132 C ARG G 18 -34.542 9.579 -17.490 1.00 56.92 ATOM 133 O ARG G 18 -33.695 8.887 -16.928 1.00 58.15 ATOM 134 CB ARG G 18 -34.032 11.089 -19.406 1.00 60.82 ATOM 135 CG ARG G 18 -33.004 10.123 -19.956 1.00 66.72 ATOM 136 CD ARG G 18 -33.132 10.040 -21.468 1.00 71.79 ATOM 137 NE ARG G 18 -31.924 9.542 -22.116 1.00 77.69 ATOM 138 CZ ARG G 18 -31.160 10.271 -22.924 1.00 83.84 ATOM 139 NH1 ARG G 18 -31.484 11.530 -23.192 1.00 85.78 ATOM 140 NH2 ARG G 18 -30.077 9.740 -23.474 1.00 79.85 ATOM 141 N CYS G 19 -35.759 9.139 -17.765 1.00 53.29 ATOM 142 CA CYS G 19 -36.141 7.782 -17.424 1.00 49.06 ATOM 143 C CYS G 19 -35.617 6.767 -18.424 1.00 46.75 ATOM 144 O CYS G 19 -35.447 7.053 -19.606 1.00 48.13 ATOM 145 CB CYS G 19 -37.661 7.672 -17.328 1.00 49.47 ATOM 146 SG CYS G 19 -38.362 8.656 -15.992 1.00 73.38 ATOM 147 N ALA G 20 -35.464 5.388 -17.932 1.00 23.11 ATOM 148 CA ALA G 20 -35.158 4.201 -18.714 1.00 21.13 ATOM 149 C ALA G 20 -36.134 3.155 -18.207 1.00 19.11 ATOM 150 O ALA G 20 -35.838 2.429 -17.265 1.00 21.03 ATOM 151 CB ALA G 20 -33.732 3.763 -18.466 1.00 21.22 ATOM 152 N DPR G 21 -37.314 3.115 -18.784 1.00 19.45 ATOM 153 CA DPR G 21 -38.380 2.294 -18.210 1.00 19.58 ATOM 154 CB DPR G 21 -39.529 2.459 -19.209 1.00 21.72 ATOM 155 CG DPR G 21 -39.287 3.768 -19.832 1.00 24.95 ATOM 156 CD DPR G 21 -37.806 3.961 -19.885 1.00 25.75 ATOM 157 C DPR G 21 -38.745 2.829 -16.838 1.00 19.86 ATOM 158 O DPR G 21 -39.080 4.007 -16.710 1.00 22.94 ATOM 159 N THR G 22 -38.612 1.986 -15.838 1.00 20.34 ATOM 160 CA THR G 22 -38.949 2.342 -14.465 1.00 19.04 ATOM 161 C THR G 22 -37.729 2.829 -13.679 1.00 21.36 ATOM 162 O THR G 22 -37.822 3.103 -12.480 1.00 22.56 ATOM 163 CB THR G 22 -39.513 1.138 -13.723 1.00 20.02 ATOM 164 OG1 THR G 22 -38.522 0.107 -13.713 1.00 20.69 ATOM 165 CG2 THR G 22 -40.799 0.626 -14.390 1.00 20.34 ATOM 166 N U2X G 23 -36.459 3.107 -14.366 1.00 41.09 ATOM 167 C U2X G 23 -34.798 4.918 -14.069 1.00 44.98 ATOM 168 O U2X G 23 -35.148 5.449 -15.118 1.00 47.28 ATOM 169 CA U2X G 23 -35.229 3.522 -13.749 1.00 39.59 ATOM 170 CB U2X G 23 -34.088 2.585 -13.968 1.00 40.23 ATOM 171 CG U2X G 23 -34.284 1.107 -13.818 1.00 44.93 ATOM 172 CD1 U2X G 23 -34.220 0.521 -12.526 1.00 40.65 ATOM 173 CD2 U2X G 23 -34.481 0.313 -14.945 1.00 40.23 ATOM 174 CE1 U2X G 23 -34.368 -0.930 -12.376 1.00 36.63 ATOM 175 CE2 U2X G 23 -34.637 -1.190 -14.788 1.00 43.04 ATOM 176 CZ U2X G 23 -34.578 -1.752 -13.538 1.00 39.49 ATOM 177 OH U2X G 23 -34.704 -3.126 -13.390 1.00 42.10 ATOM 178 C7 U2X G 23 -34.179 -3.741 -12.264 1.00 43.28 ATOM 179 C1 U2X G 23 -32.661 -7.251 -11.662 1.00 50.61 ATOM 180 C2 U2X G 23 -33.787 -6.260 -11.532 1.00 50.29 ATOM 181 C3 U2X G 23 -33.453 -5.043 -12.463 1.00 35.80 ATOM 182 C4 U2X G 23 -33.206 -5.538 -13.950 1.00 58.63 ATOM 183 C5 U2X G 23 -32.183 -6.709 -13.970 1.00 37.68 ATOM 184 C6 U2X G 23 -32.681 -7.783 -13.046 1.00 45.68 ATOM 185 N CYS G 24 -34.020 5.504 -13.196 1.00 42.22 ATOM 186 CA CYS G 24 -33.430 6.808 -13.462 1.00 45.16 ATOM 187 C CYS G 24 -32.073 6.667 -14.141 1.00 47.83 ATOM 188 O CYS G 24 -31.201 5.936 -13.666 1.00 44.45 ATOM 189 CB CYS G 24 -33.278 7.609 -12.175 1.00 51.28 ATOM 190 SG CYS G 24 -32.380 9.154 -12.408 1.00 60.63 ATOM 191 N ALA G 25 -31.908 7.359 -15.264 1.00 46.96 ATOM 192 CA ALA G 25 -30.636 7.378 -15.972 1.00 45.98 ATOM 193 C ALA G 25 -30.138 8.812 -16.097 1.00 51.45 ATOM 194 O ALA G 25 -30.907 9.712 -16.428 1.00 53.50 ATOM 195 CB ALA G 25 -30.776 6.741 -17.341 1.00 45.84 ATOM 196 N CYS G 26 -28.864 9.030 -15.818 1.00 48.37 ATOM 197 CA CYS G 26 -28.296 10.356 -15.941 1.00 49.39 ATOM 198 C CYS G 26 -27.538 10.454 -17.261 1.00 54.22 ATOM 199 O CYS G 26 -26.751 9.581 -17.602 1.00 51.15 ATOM 200 CB CYS G 26 -27.412 10.675 -14.741 1.00 54.07 ATOM 201 SG CYS G 26 -28.340 10.863 -13.201 1.00 67.51 ATOM 202 N VAL G 27 -27.823 11.500 -18.021 1.00 43.98 ATOM 203 CA VAL G 27 -27.285 11.642 -19.361 1.00 47.81 ATOM 204 C VAL G 27 -26.442 12.906 -19.553 1.00 49.50 ATOM 205 O VAL G 27 -26.659 13.918 -18.895 1.00 45.87 ATOM 206 CB VAL G 27 -28.410 11.598 -20.400 1.00 51.77 ATOM 207 CG1 VAL G 27 -27.858 11.838 -21.791 1.00 56.04 ATOM 208 CG2 VAL G 27 -29.111 10.257 -20.337 1.00 58.83 ATOM 209 N NH2 G 28 -25.624 12.702 -20.553 1.00 63.13 TER