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 B 20 492 PDB 4LAJ 4LAJ 20 492 DBREF 4LAJ C 1 28 PDB 4LAJ 4LAJ 1 28 MODRES 4LAJ U2X C 23 TYR O-(CYCLOHEXYLMETHYL)-L-TYROSINE SEQRES 1 C 28 MPT ASN LEU HIS PHE CYS GLN LEU ARG CYS LYS SER LEU SEQRES 2 C 28 GLY LEU LEU GLY ARG CYS ALA DPR THR TYR CYS ALA CYS SEQRES 3 C 28 VAL NH2 ATOM 1 C1 EDO B 509 3.590 37.123 -62.833 1.00 58.51 ATOM 2 O1 EDO B 509 4.317 38.207 -62.250 1.00 59.63 ATOM 3 C2 EDO B 509 4.282 36.678 -64.120 1.00 61.56 ATOM 4 O2 EDO B 509 5.613 36.252 -63.823 1.00 61.27 TER ATOM 1 CA MPT C 1 3.415 50.592 -60.964 1.00 36.42 ATOM 2 C MPT C 1 4.112 51.701 -61.674 1.00 43.49 ATOM 3 O MPT C 1 4.868 52.467 -61.017 1.00 48.23 ATOM 4 CB MPT C 1 1.974 50.780 -60.640 1.00 36.73 ATOM 5 SG MPT C 1 1.472 52.378 -60.084 1.00 48.73 ATOM 6 N ASN C 2 3.808 52.017 -63.015 1.00 45.52 ATOM 7 CA ASN C 2 4.352 53.369 -63.084 1.00 54.81 ATOM 8 C ASN C 2 3.254 54.405 -62.820 1.00 52.68 ATOM 9 O ASN C 2 2.212 54.419 -63.482 1.00 41.71 ATOM 10 CB ASN C 2 5.052 53.629 -64.426 1.00 69.54 ATOM 11 CG ASN C 2 4.088 53.891 -65.559 1.00 74.36 ATOM 12 OD1 ASN C 2 3.437 52.977 -66.067 1.00 74.40 ATOM 13 ND2 ASN C 2 3.974 55.160 -65.948 1.00 69.43 ATOM 14 N LEU C 3 3.500 55.264 -61.834 1.00 48.95 ATOM 15 CA LEU C 3 2.462 56.103 -61.237 1.00 52.21 ATOM 16 C LEU C 3 1.791 57.042 -62.233 1.00 53.48 ATOM 17 O LEU C 3 0.569 57.192 -62.217 1.00 59.60 ATOM 18 CB LEU C 3 3.056 56.914 -60.081 1.00 52.12 ATOM 19 CG LEU C 3 2.076 57.672 -59.181 1.00 53.28 ATOM 20 CD1 LEU C 3 0.995 56.725 -58.671 1.00 50.75 ATOM 21 CD2 LEU C 3 2.825 58.311 -58.022 1.00 53.37 ATOM 22 N HIS C 4 2.585 57.682 -63.085 1.00 54.44 ATOM 23 CA HIS C 4 2.049 58.651 -64.036 1.00 64.80 ATOM 24 C HIS C 4 1.007 58.042 -64.972 1.00 61.39 ATOM 25 O HIS C 4 -0.064 58.614 -65.168 1.00 64.52 ATOM 26 CB HIS C 4 3.181 59.267 -64.860 1.00 72.57 ATOM 27 CG HIS C 4 2.710 60.229 -65.903 1.00 75.78 ATOM 28 ND1 HIS C 4 2.686 59.917 -67.249 1.00 77.83 ATOM 29 CD2 HIS C 4 2.234 61.492 -65.807 1.00 77.62 ATOM 30 CE1 HIS C 4 2.223 60.946 -67.930 1.00 79.76 ATOM 31 NE2 HIS C 4 1.940 61.918 -67.078 1.00 77.84 ATOM 32 N PHE C 5 1.318 56.884 -65.543 1.00 60.62 ATOM 33 CA PHE C 5 0.394 56.226 -66.462 1.00 57.73 ATOM 34 C PHE C 5 -0.833 55.723 -65.712 1.00 52.02 ATOM 35 O PHE C 5 -1.946 55.733 -66.238 1.00 51.25 ATOM 36 CB PHE C 5 1.084 55.072 -67.193 1.00 66.99 ATOM 37 CG PHE C 5 0.202 54.370 -68.194 1.00 77.12 ATOM 38 CD1 PHE C 5 -0.217 55.023 -69.342 1.00 79.92 ATOM 39 CD2 PHE C 5 -0.197 53.055 -67.994 1.00 79.51 ATOM 40 CE1 PHE C 5 -1.026 54.384 -70.268 1.00 78.71 ATOM 41 CE2 PHE C 5 -1.002 52.410 -68.918 1.00 77.04 ATOM 42 CZ PHE C 5 -1.419 53.077 -70.055 1.00 78.01 ATOM 43 N CYS C 6 -0.621 55.294 -64.473 1.00 41.74 ATOM 44 CA CYS C 6 -1.709 54.790 -63.651 1.00 42.56 ATOM 45 C CYS C 6 -2.711 55.888 -63.349 1.00 48.23 ATOM 46 O CYS C 6 -3.921 55.697 -63.462 1.00 48.91 ATOM 47 CB CYS C 6 -1.167 54.215 -62.345 1.00 40.60 ATOM 48 SG CYS C 6 -2.453 53.769 -61.163 1.00 51.53 ATOM 49 N GLN C 7 -2.192 57.046 -62.970 1.00 44.60 ATOM 50 CA GLN C 7 -3.032 58.181 -62.638 1.00 46.16 ATOM 51 C GLN C 7 -3.742 58.701 -63.882 1.00 48.07 ATOM 52 O GLN C 7 -4.881 59.157 -63.800 1.00 54.02 ATOM 53 CB GLN C 7 -2.195 59.265 -61.958 1.00 45.26 ATOM 54 CG GLN C 7 -1.723 58.815 -60.579 1.00 56.20 ATOM 55 CD GLN C 7 -0.934 59.865 -59.835 1.00 62.58 ATOM 56 OE1 GLN C 7 -0.267 60.705 -60.441 1.00 61.81 ATOM 57 NE2 GLN C 7 -1.004 59.823 -58.506 1.00 61.81 ATOM 58 N LEU C 8 -3.080 58.617 -65.034 1.00 54.28 ATOM 59 CA LEU C 8 -3.713 58.984 -66.298 1.00 54.40 ATOM 60 C LEU C 8 -4.901 58.073 -66.595 1.00 51.07 ATOM 61 O LEU C 8 -5.993 58.543 -66.901 1.00 59.73 ATOM 62 CB LEU C 8 -2.707 58.922 -67.453 1.00 53.26 ATOM 63 CG LEU C 8 -2.095 60.235 -67.957 1.00 65.89 ATOM 64 CD1 LEU C 8 -1.404 61.002 -66.836 1.00 73.88 ATOM 65 CD2 LEU C 8 -1.131 59.984 -69.108 1.00 64.83 ATOM 66 N ARG C 9 -4.684 56.768 -66.496 1.00 55.37 ATOM 67 CA ARG C 9 -5.740 55.797 -66.769 1.00 54.00 ATOM 68 C ARG C 9 -6.906 55.930 -65.797 1.00 49.13 ATOM 69 O ARG C 9 -8.066 55.934 -66.208 1.00 51.09 ATOM 70 CB ARG C 9 -5.196 54.372 -66.723 1.00 57.27 ATOM 71 CG ARG C 9 -4.420 53.963 -67.954 1.00 65.70 ATOM 72 CD ARG C 9 -3.904 52.547 -67.796 1.00 79.92 ATOM 73 NE ARG C 9 -4.978 51.618 -67.451 1.00 90.15 ATOM 74 CZ ARG C 9 -4.790 50.451 -66.843 1.00 91.86 ATOM 75 NH1 ARG C 9 -3.565 50.065 -66.511 1.00 97.74 ATOM 76 NH2 ARG C 9 -5.826 49.667 -66.567 1.00 80.94 ATOM 77 N CYS C 10 -6.597 56.016 -64.507 1.00 41.75 ATOM 78 CA CYS C 10 -7.637 56.108 -63.491 1.00 43.43 ATOM 79 C CYS C 10 -8.404 57.423 -63.603 1.00 47.72 ATOM 80 O CYS C 10 -9.594 57.465 -63.302 1.00 46.80 ATOM 81 CB CYS C 10 -7.044 55.944 -62.089 1.00 36.96 ATOM 82 SG CYS C 10 -6.259 54.334 -61.811 1.00 45.31 ATOM 83 N LYS C 11 -7.735 58.488 -64.041 1.00 52.49 ATOM 84 CA LYS C 11 -8.434 59.748 -64.308 1.00 55.14 ATOM 85 C LYS C 11 -9.587 59.586 -65.281 1.00 58.91 ATOM 86 O LYS C 11 -10.636 60.208 -65.119 1.00 65.78 ATOM 87 CB LYS C 11 -7.493 60.809 -64.872 1.00 60.25 ATOM 88 CG LYS C 11 -8.116 62.198 -64.849 1.00 65.50 ATOM 89 CD LYS C 11 -7.146 63.286 -65.246 1.00 69.18 ATOM 90 CE LYS C 11 -7.864 64.330 -66.101 1.00 76.25 ATOM 91 NZ LYS C 11 -9.227 64.671 -65.593 1.00 77.55 ATOM 92 N SER C 12 -9.388 58.753 -66.295 1.00 59.24 ATOM 93 CA SER C 12 -10.412 58.541 -67.304 1.00 66.99 ATOM 94 C SER C 12 -11.647 57.899 -66.678 1.00 74.99 ATOM 95 O SER C 12 -12.740 57.960 -67.242 1.00 82.26 ATOM 96 CB SER C 12 -9.873 57.679 -68.449 1.00 72.78 ATOM 97 OG SER C 12 -9.780 56.316 -68.072 1.00 78.56 ATOM 98 N LEU C 13 -11.468 57.286 -65.511 1.00 69.24 ATOM 99 CA LEU C 13 -12.580 56.675 -64.791 1.00 62.16 ATOM 100 C LEU C 13 -13.128 57.601 -63.711 1.00 62.41 ATOM 101 O LEU C 13 -14.072 57.248 -63.008 1.00 61.74 ATOM 102 CB LEU C 13 -12.152 55.351 -64.155 1.00 66.71 ATOM 103 CG LEU C 13 -11.603 54.267 -65.084 1.00 72.89 ATOM 104 CD1 LEU C 13 -11.303 52.983 -64.314 1.00 71.28 ATOM 105 CD2 LEU C 13 -12.574 54.011 -66.224 1.00 76.80 ATOM 106 N GLY C 14 -12.540 58.787 -63.584 1.00 57.16 ATOM 107 CA GLY C 14 -12.964 59.728 -62.563 1.00 48.03 ATOM 108 C GLY C 14 -12.348 59.395 -61.218 1.00 43.17 ATOM 109 O GLY C 14 -12.838 59.819 -60.172 1.00 46.36 ATOM 110 N LEU C 15 -11.263 58.631 -61.248 1.00 41.04 ATOM 111 CA LEU C 15 -10.631 58.152 -60.025 1.00 46.94 ATOM 112 C LEU C 15 -9.176 58.586 -59.880 1.00 44.89 ATOM 113 O LEU C 15 -8.512 58.926 -60.856 1.00 46.37 ATOM 114 CB LEU C 15 -10.711 56.629 -59.961 1.00 44.87 ATOM 115 CG LEU C 15 -12.103 56.028 -60.142 1.00 44.61 ATOM 116 CD1 LEU C 15 -12.037 54.514 -60.006 1.00 44.76 ATOM 117 CD2 LEU C 15 -13.061 56.620 -59.132 1.00 47.25 ATOM 118 N LEU C 16 -8.697 58.554 -58.642 1.00 43.95 ATOM 119 CA LEU C 16 -7.291 58.753 -58.335 1.00 40.07 ATOM 120 C LEU C 16 -6.500 57.507 -58.704 1.00 43.12 ATOM 121 O LEU C 16 -7.041 56.404 -58.724 1.00 40.17 ATOM 122 CB LEU C 16 -7.101 59.060 -56.849 1.00 38.32 ATOM 123 CG LEU C 16 -7.950 60.165 -56.225 1.00 49.47 ATOM 124 CD1 LEU C 16 -7.783 60.164 -54.714 1.00 53.47 ATOM 125 CD2 LEU C 16 -7.580 61.523 -56.796 1.00 52.87 ATOM 126 N GLY C 17 -5.223 57.681 -59.021 1.00 43.93 ATOM 127 CA GLY C 17 -4.366 56.537 -59.257 1.00 43.32 ATOM 128 C GLY C 17 -3.280 56.440 -58.203 1.00 46.06 ATOM 129 O GLY C 17 -2.666 57.445 -57.846 1.00 51.99 ATOM 130 N ARG C 18 -3.051 55.238 -57.687 1.00 40.51 ATOM 131 CA ARG C 18 -1.886 55.001 -56.847 1.00 39.23 ATOM 132 C ARG C 18 -1.364 53.600 -57.075 1.00 48.65 ATOM 133 O ARG C 18 -2.078 52.730 -57.568 1.00 50.29 ATOM 134 CB ARG C 18 -2.195 55.213 -55.363 1.00 46.26 ATOM 135 CG ARG C 18 -3.138 54.208 -54.723 1.00 50.92 ATOM 136 CD ARG C 18 -3.065 54.346 -53.203 1.00 62.04 ATOM 137 NE ARG C 18 -4.238 53.824 -52.504 1.00 72.74 ATOM 138 CZ ARG C 18 -5.096 54.581 -51.821 1.00 82.40 ATOM 139 NH1 ARG C 18 -4.911 55.894 -51.739 1.00 87.85 ATOM 140 NH2 ARG C 18 -6.136 54.027 -51.213 1.00 80.99 ATOM 141 N CYS C 19 -0.106 53.380 -56.722 1.00 44.18 ATOM 142 CA CYS C 19 0.470 52.065 -56.885 1.00 41.01 ATOM 143 C CYS C 19 0.063 51.145 -55.745 1.00 40.37 ATOM 144 O CYS C 19 -0.123 51.568 -54.607 1.00 40.13 ATOM 145 CB CYS C 19 1.994 52.159 -56.976 1.00 43.81 ATOM 146 SG CYS C 19 2.579 53.038 -58.444 1.00 59.67 ATOM 147 N ALA C 20 0.101 49.679 -55.863 1.00 23.11 ATOM 148 CA ALA C 20 -0.099 48.548 -54.971 1.00 21.13 ATOM 149 C ALA C 20 0.987 47.562 -55.364 1.00 19.11 ATOM 150 O ALA C 20 0.784 46.722 -56.232 1.00 21.03 ATOM 151 CB ALA C 20 -1.468 47.944 -55.188 1.00 21.22 ATOM 152 N DPR C 21 2.155 47.700 -54.775 1.00 19.45 ATOM 153 CA DPR C 21 3.308 46.939 -55.257 1.00 19.58 ATOM 154 CB DPR C 21 4.416 47.318 -54.268 1.00 21.72 ATOM 155 CG DPR C 21 4.031 48.649 -53.779 1.00 24.95 ATOM 156 CD DPR C 21 2.538 48.694 -53.758 1.00 25.75 ATOM 157 C DPR C 21 3.643 47.374 -56.671 1.00 19.86 ATOM 158 O DPR C 21 3.860 48.562 -56.912 1.00 22.94 ATOM 159 N THR C 22 3.615 46.429 -57.584 1.00 20.34 ATOM 160 CA THR C 22 3.940 46.683 -58.983 1.00 19.04 ATOM 161 C THR C 22 2.692 46.964 -59.823 1.00 21.36 ATOM 162 O THR C 22 2.779 47.129 -61.043 1.00 22.56 ATOM 163 CB THR C 22 4.636 45.477 -59.598 1.00 20.02 ATOM 164 OG1 THR C 22 3.755 44.354 -59.515 1.00 20.69 ATOM 165 CG2 THR C 22 5.954 45.166 -58.872 1.00 20.34 ATOM 166 N U2X C 23 1.421 47.103 -59.273 1.00 29.64 ATOM 167 C U2X C 23 -0.452 48.670 -59.807 1.00 39.67 ATOM 168 O U2X C 23 -0.272 49.355 -58.801 1.00 36.17 ATOM 169 CA U2X C 23 0.169 47.314 -59.942 1.00 35.10 ATOM 170 CB U2X C 23 -0.864 46.303 -59.588 1.00 35.39 ATOM 171 CG U2X C 23 -0.494 44.855 -59.537 1.00 41.88 ATOM 172 CD1 U2X C 23 -0.438 44.108 -60.741 1.00 35.68 ATOM 173 CD2 U2X C 23 -0.273 44.242 -58.308 1.00 50.72 ATOM 174 CE1 U2X C 23 -0.135 42.678 -60.691 1.00 32.26 ATOM 175 CE2 U2X C 23 0.043 42.759 -58.253 1.00 46.29 ATOM 176 CZ U2X C 23 0.101 42.044 -59.422 1.00 39.96 ATOM 177 OH U2X C 23 0.338 40.682 -59.388 1.00 41.62 ATOM 178 C7 U2X C 23 0.041 39.951 -60.525 1.00 44.44 ATOM 179 C1 U2X C 23 -0.374 36.106 -60.772 1.00 43.61 ATOM 180 C2 U2X C 23 0.468 37.348 -60.634 1.00 43.27 ATOM 181 C3 U2X C 23 -0.477 38.559 -60.324 1.00 38.84 ATOM 182 C4 U2X C 23 -1.346 38.262 -59.031 1.00 40.14 ATOM 183 C5 U2X C 23 -2.047 36.887 -59.202 1.00 25.64 ATOM 184 C6 U2X C 23 -1.001 35.842 -59.455 1.00 34.01 ATOM 185 N CYS C 24 -1.218 49.038 -60.788 1.00 36.53 ATOM 186 CA CYS C 24 -2.005 50.257 -60.725 1.00 40.42 ATOM 187 C CYS C 24 -3.353 50.032 -60.045 1.00 37.54 ATOM 188 O CYS C 24 -4.112 49.139 -60.419 1.00 39.79 ATOM 189 CB CYS C 24 -2.235 50.824 -62.120 1.00 39.85 ATOM 190 SG CYS C 24 -3.370 52.225 -62.125 1.00 56.32 ATOM 191 N ALA C 25 -3.652 50.856 -59.051 1.00 36.95 ATOM 192 CA ALA C 25 -4.942 50.785 -58.390 1.00 41.47 ATOM 193 C ALA C 25 -5.653 52.123 -58.535 1.00 43.61 ATOM 194 O ALA C 25 -5.054 53.180 -58.334 1.00 42.47 ATOM 195 CB ALA C 25 -4.776 50.413 -56.926 1.00 38.62 ATOM 196 N CYS C 26 -6.932 52.073 -58.873 1.00 39.58 ATOM 197 CA CYS C 26 -7.754 53.266 -58.961 1.00 40.14 ATOM 198 C CYS C 26 -8.506 53.460 -57.655 1.00 46.80 ATOM 199 O CYS C 26 -8.997 52.509 -57.067 1.00 46.80 ATOM 200 CB CYS C 26 -8.732 53.164 -60.116 1.00 37.36 ATOM 201 SG CYS C 26 -7.970 53.107 -61.738 1.00 53.81 ATOM 202 N VAL C 27 -8.570 54.698 -57.195 1.00 43.98 ATOM 203 CA VAL C 27 -9.147 55.012 -55.902 1.00 47.81 ATOM 204 C VAL C 27 -10.136 56.176 -55.978 1.00 49.50 ATOM 205 O VAL C 27 -9.918 57.146 -56.693 1.00 45.87 ATOM 206 CB VAL C 27 -8.039 55.335 -54.897 1.00 51.77 ATOM 207 CG1 VAL C 27 -8.623 55.822 -53.583 1.00 56.04 ATOM 208 CG2 VAL C 27 -7.160 54.119 -54.690 1.00 58.83 ATOM 209 N NH2 C 28 -11.499 55.746 -55.600 1.00 63.13 TER