0.019482 0.000000 0.000000 0.000000 0.010947 0.000000 0.000000 0.000000 0.009242 0.00000 0.00000 0.00000 Li, H. Margulies, D.H. Mariuzza, R.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 51.330 91.350 108.200 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK J.Mol.Biol. JMOBAK 0070 0022-2836 283 179 191 10.1006/jmbi.1998.2091 9761682 Three-dimensional structure of H-2Dd complexed with an immunodominant peptide from human immunodeficiency virus envelope glycoprotein 120. 1998 US J.Exp.Med. JEMEAV 0774 0022-1007 178 1877 H-2Dd Exploits a Four Residue Peptide Binding Motif 1993 10.2210/pdb1ddh/pdb pdb_00001ddh 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 IMAGE PLATE 1997-07 MAR scanner 300 mm plate M x-ray 1 0.773 1.0 BL9-1 SSRL 0.773 SYNCHROTRON SSRL BEAMLINE BL9-1 31862.404 MHC CLASS I H-2DD HEAVY CHAIN EXTRACELLULAR DOMAINS G1M 1 man polymer 11678.388 BETA-2 MICROGLOBULIN EXTRACELLULAR DOMAIN I1M 1 man polymer 1075.265 HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120 RESIDUES 308-322 1 man polymer 18.015 water 4 nat water no no MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWERETRRANGNEQSFRVDLRT ALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYL EGECVEWLRRYLKNGNATLLATDPPKAHVTHHRRPEGDVTLRCWALGFYPAEITLTWQLNGEELTQEMELVETRPAGDGT FQKWASVVVPLGKQQKYTCHVEHEGLPEPLTLRW MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWERETRRANGNEQSFRVDLRT ALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYL EGECVEWLRRYLKNGNATLLATDPPKAHVTHHRRPEGDVTLRCWALGFYPAEITLTWQLNGEELTQEMELVETRPAGDGT FQKWASVVVPLGKQQKYTCHVEHEGLPEPLTLRW A polypeptide(L) no no MQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYAC RVKHASMAEPKTVYWDRDM MQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYAC RVKHASMAEPKTVYWDRDM B polypeptide(L) no no RGPGRAFVTI RGPGRAFVTI P polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n house mouse Mus Escherichia Escherichia coli sample BL21 EXTRACELLULAR 10090 Mus musculus INCLUSION BODY 469008 Escherichia coli BL21(DE3) BL21 (DE3) BACTERIAL PET3A house mouse Mus Escherichia Escherichia coli sample BL21 EXTRACELLULAR 10090 Mus musculus INCLUSION BODY 469008 Escherichia coli BL21(DE3) BL21 (DE3) BACTERIAL PET21D Lentivirus sample 11676 Human immunodeficiency virus 1 1 2.53 58 6.5 pH 6.5 database_2 pdbx_initial_refinement_model struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Database references Refinement description 1 0 1999-01-13 1 1 2008-03-24 1 2 2011-07-13 1 3 2023-08-09 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details Y BNL 1998-06-22 REL REL HOH water 1VAD PDB ENTRY 1VAD PDB experimental model HOH 1 4 HOH HOH 275 A HOH 2 4 HOH HOH 276 A HOH 3 4 HOH HOH 277 A HOH 4 4 HOH HOH 278 A MET 1 n 1 MET 1 A SER 2 n 2 SER 2 A HIS 3 n 3 HIS 3 A SER 4 n 4 SER 4 A LEU 5 n 5 LEU 5 A ARG 6 n 6 ARG 6 A TYR 7 n 7 TYR 7 A PHE 8 n 8 PHE 8 A VAL 9 n 9 VAL 9 A THR 10 n 10 THR 10 A ALA 11 n 11 ALA 11 A VAL 12 n 12 VAL 12 A SER 13 n 13 SER 13 A ARG 14 n 14 ARG 14 A PRO 15 n 15 PRO 15 A GLY 16 n 16 GLY 16 A PHE 17 n 17 PHE 17 A GLY 18 n 18 GLY 18 A GLU 19 n 19 GLU 19 A PRO 20 n 20 PRO 20 A ARG 21 n 21 ARG 21 A TYR 22 n 22 TYR 22 A MET 23 n 23 MET 23 A GLU 24 n 24 GLU 24 A VAL 25 n 25 VAL 25 A GLY 26 n 26 GLY 26 A TYR 27 n 27 TYR 27 A VAL 28 n 28 VAL 28 A ASP 29 n 29 ASP 29 A ASN 30 n 30 ASN 30 A THR 31 n 31 THR 31 A GLU 32 n 32 GLU 32 A PHE 33 n 33 PHE 33 A VAL 34 n 34 VAL 34 A ARG 35 n 35 ARG 35 A PHE 36 n 36 PHE 36 A ASP 37 n 37 ASP 37 A SER 38 n 38 SER 38 A ASP 39 n 39 ASP 39 A ALA 40 n 40 ALA 40 A GLU 41 n 41 GLU 41 A ASN 42 n 42 ASN 42 A PRO 43 n 43 PRO 43 A ARG 44 n 44 ARG 44 A TYR 45 n 45 TYR 45 A GLU 46 n 46 GLU 46 A PRO 47 n 47 PRO 47 A ARG 48 n 48 ARG 48 A ALA 49 n 49 ALA 49 A ARG 50 n 50 ARG 50 A TRP 51 n 51 TRP 51 A ILE 52 n 52 ILE 52 A GLU 53 n 53 GLU 53 A GLN 54 n 54 GLN 54 A GLU 55 n 55 GLU 55 A GLY 56 n 56 GLY 56 A PRO 57 n 57 PRO 57 A GLU 58 n 58 GLU 58 A TYR 59 n 59 TYR 59 A TRP 60 n 60 TRP 60 A GLU 61 n 61 GLU 61 A ARG 62 n 62 ARG 62 A GLU 63 n 63 GLU 63 A THR 64 n 64 THR 64 A ARG 65 n 65 ARG 65 A ARG 66 n 66 ARG 66 A ALA 67 n 67 ALA 67 A ASN 68 n 68 ASN 68 A GLY 69 n 69 GLY 69 A ASN 70 n 70 ASN 70 A GLU 71 n 71 GLU 71 A GLN 72 n 72 GLN 72 A SER 73 n 73 SER 73 A PHE 74 n 74 PHE 74 A ARG 75 n 75 ARG 75 A VAL 76 n 76 VAL 76 A ASP 77 n 77 ASP 77 A LEU 78 n 78 LEU 78 A ARG 79 n 79 ARG 79 A THR 80 n 80 THR 80 A ALA 81 n 81 ALA 81 A LEU 82 n 82 LEU 82 A ARG 83 n 83 ARG 83 A TYR 84 n 84 TYR 84 A TYR 85 n 85 TYR 85 A ASN 86 n 86 ASN 86 A GLN 87 n 87 GLN 87 A SER 88 n 88 SER 88 A ALA 89 n 89 ALA 89 A GLY 90 n 90 GLY 90 A GLY 91 n 91 GLY 91 A SER 92 n 92 SER 92 A HIS 93 n 93 HIS 93 A THR 94 n 94 THR 94 A LEU 95 n 95 LEU 95 A GLN 96 n 96 GLN 96 A TRP 97 n 97 TRP 97 A MET 98 n 98 MET 98 A ALA 99 n 99 ALA 99 A GLY 100 n 100 GLY 100 A CYS 101 n 101 CYS 101 A ASP 102 n 102 ASP 102 A VAL 103 n 103 VAL 103 A GLU 104 n 104 GLU 104 A SER 105 n 105 SER 105 A ASP 106 n 106 ASP 106 A GLY 107 n 107 GLY 107 A ARG 108 n 108 ARG 108 A LEU 109 n 109 LEU 109 A LEU 110 n 110 LEU 110 A ARG 111 n 111 ARG 111 A GLY 112 n 112 GLY 112 A TYR 113 n 113 TYR 113 A TRP 114 n 114 TRP 114 A GLN 115 n 115 GLN 115 A PHE 116 n 116 PHE 116 A ALA 117 n 117 ALA 117 A TYR 118 n 118 TYR 118 A ASP 119 n 119 ASP 119 A GLY 120 n 120 GLY 120 A CYS 121 n 121 CYS 121 A ASP 122 n 122 ASP 122 A TYR 123 n 123 TYR 123 A ILE 124 n 124 ILE 124 A ALA 125 n 125 ALA 125 A LEU 126 n 126 LEU 126 A ASN 127 n 127 ASN 127 A GLU 128 n 128 GLU 128 A ASP 129 n 129 ASP 129 A LEU 130 n 130 LEU 130 A LYS 131 n 131 LYS 131 A THR 132 n 132 THR 132 A TRP 133 n 133 TRP 133 A THR 134 n 134 THR 134 A ALA 135 n 135 ALA 135 A ALA 136 n 136 ALA 136 A ASP 137 n 137 ASP 137 A MET 138 n 138 MET 138 A ALA 139 n 139 ALA 139 A ALA 140 n 140 ALA 140 A GLN 141 n 141 GLN 141 A ILE 142 n 142 ILE 142 A THR 143 n 143 THR 143 A ARG 144 n 144 ARG 144 A ARG 145 n 145 ARG 145 A LYS 146 n 146 LYS 146 A TRP 147 n 147 TRP 147 A GLU 148 n 148 GLU 148 A GLN 149 n 149 GLN 149 A ALA 150 n 150 ALA 150 A GLY 151 n 151 GLY 151 A ALA 152 n 152 ALA 152 A ALA 153 n 153 ALA 153 A GLU 154 n 154 GLU 154 A ARG 155 n 155 ARG 155 A ASP 156 n 156 ASP 156 A ARG 157 n 157 ARG 157 A ALA 158 n 158 ALA 158 A TYR 159 n 159 TYR 159 A LEU 160 n 160 LEU 160 A GLU 161 n 161 GLU 161 A GLY 162 n 162 GLY 162 A GLU 163 n 163 GLU 163 A CYS 164 n 164 CYS 164 A VAL 165 n 165 VAL 165 A GLU 166 n 166 GLU 166 A TRP 167 n 167 TRP 167 A LEU 168 n 168 LEU 168 A ARG 169 n 169 ARG 169 A ARG 170 n 170 ARG 170 A TYR 171 n 171 TYR 171 A LEU 172 n 172 LEU 172 A LYS 173 n 173 LYS 173 A ASN 174 n 174 ASN 174 A GLY 175 n 175 GLY 175 A ASN 176 n 176 ASN 176 A ALA 177 n 177 ALA 177 A THR 178 n 178 THR 178 A LEU 179 n 179 LEU 179 A LEU 180 n 180 LEU 180 A ALA 181 n 181 ALA 181 A THR 182 n 182 THR 182 A ASP 183 n 183 ASP 183 A PRO 184 n 184 PRO 184 A PRO 185 n 185 PRO 185 A LYS 186 n 186 LYS 186 A ALA 187 n 187 ALA 187 A HIS 188 n 188 HIS 188 A VAL 189 n 189 VAL 189 A THR 190 n 190 THR 190 A HIS 191 n 191 HIS 191 A HIS 192 n 192 HIS 192 A ARG 193 n 193 ARG 193 A ARG 194 n 194 ARG 194 A PRO 195 n 195 PRO 195 A GLU 196 n 196 GLU 196 A GLY 197 n 197 GLY 197 A ASP 198 n 198 ASP 198 A VAL 199 n 199 VAL 199 A THR 200 n 200 THR 200 A LEU 201 n 201 LEU 201 A ARG 202 n 202 ARG 202 A CYS 203 n 203 CYS 203 A TRP 204 n 204 TRP 204 A ALA 205 n 205 ALA 205 A LEU 206 n 206 LEU 206 A GLY 207 n 207 GLY 207 A PHE 208 n 208 PHE 208 A TYR 209 n 209 TYR 209 A PRO 210 n 210 PRO 210 A ALA 211 n 211 ALA 211 A GLU 212 n 212 GLU 212 A ILE 213 n 213 ILE 213 A THR 214 n 214 THR 214 A LEU 215 n 215 LEU 215 A THR 216 n 216 THR 216 A TRP 217 n 217 TRP 217 A GLN 218 n 218 GLN 218 A LEU 219 n 219 LEU 219 A ASN 220 n 220 ASN 220 A GLY 221 n 221 GLY 221 A GLU 222 n 222 GLU 222 A GLU 223 n 223 GLU 223 A LEU 224 n 224 LEU 224 A THR 225 n 225 THR 225 A GLN 226 n 226 GLN 226 A GLU 227 n 227 GLU 227 A MET 228 n 228 MET 228 A GLU 229 n 229 GLU 229 A LEU 230 n 230 LEU 230 A VAL 231 n 231 VAL 231 A GLU 232 n 232 GLU 232 A THR 233 n 233 THR 233 A ARG 234 n 234 ARG 234 A PRO 235 n 235 PRO 235 A ALA 236 n 236 ALA 236 A GLY 237 n 237 GLY 237 A ASP 238 n 238 ASP 238 A GLY 239 n 239 GLY 239 A THR 240 n 240 THR 240 A PHE 241 n 241 PHE 241 A GLN 242 n 242 GLN 242 A LYS 243 n 243 LYS 243 A TRP 244 n 244 TRP 244 A ALA 245 n 245 ALA 245 A SER 246 n 246 SER 246 A VAL 247 n 247 VAL 247 A VAL 248 n 248 VAL 248 A VAL 249 n 249 VAL 249 A PRO 250 n 250 PRO 250 A LEU 251 n 251 LEU 251 A GLY 252 n 252 GLY 252 A LYS 253 n 253 LYS 253 A GLN 254 n 254 GLN 254 A GLN 255 n 255 GLN 255 A LYS 256 n 256 LYS 256 A TYR 257 n 257 TYR 257 A THR 258 n 258 THR 258 A CYS 259 n 259 CYS 259 A HIS 260 n 260 HIS 260 A VAL 261 n 261 VAL 261 A GLU 262 n 262 GLU 262 A HIS 263 n 263 HIS 263 A GLU 264 n 264 GLU 264 A GLY 265 n 265 GLY 265 A LEU 266 n 266 LEU 266 A PRO 267 n 267 PRO 267 A GLU 268 n 268 GLU 268 A PRO 269 n 269 PRO 269 A LEU 270 n 270 LEU 270 A THR 271 n 271 THR 271 A LEU 272 n 272 LEU 272 A ARG 273 n 273 ARG 273 A TRP 274 n 274 TRP 274 A MET 1 n 1 MET 1 B GLN 2 n 2 GLN 2 B LYS 3 n 3 LYS 3 B THR 4 n 4 THR 4 B PRO 5 n 5 PRO 5 B GLN 6 n 6 GLN 6 B ILE 7 n 7 ILE 7 B GLN 8 n 8 GLN 8 B VAL 9 n 9 VAL 9 B TYR 10 n 10 TYR 10 B SER 11 n 11 SER 11 B ARG 12 n 12 ARG 12 B HIS 13 n 13 HIS 13 B PRO 14 n 14 PRO 14 B PRO 15 n 15 PRO 15 B GLU 16 n 16 GLU 16 B ASN 17 n 17 ASN 17 B GLY 18 n 18 GLY 18 B LYS 19 n 19 LYS 19 B PRO 20 n 20 PRO 20 B ASN 21 n 21 ASN 21 B ILE 22 n 22 ILE 22 B LEU 23 n 23 LEU 23 B ASN 24 n 24 ASN 24 B CYS 25 n 25 CYS 25 B TYR 26 n 26 TYR 26 B VAL 27 n 27 VAL 27 B THR 28 n 28 THR 28 B GLN 29 n 29 GLN 29 B PHE 30 n 30 PHE 30 B HIS 31 n 31 HIS 31 B PRO 32 n 32 PRO 32 B PRO 33 n 33 PRO 33 B HIS 34 n 34 HIS 34 B ILE 35 n 35 ILE 35 B GLU 36 n 36 GLU 36 B ILE 37 n 37 ILE 37 B GLN 38 n 38 GLN 38 B MET 39 n 39 MET 39 B LEU 40 n 40 LEU 40 B LYS 41 n 41 LYS 41 B ASN 42 n 42 ASN 42 B GLY 43 n 43 GLY 43 B LYS 44 n 44 LYS 44 B LYS 45 n 45 LYS 45 B ILE 46 n 46 ILE 46 B PRO 47 n 47 PRO 47 B LYS 48 n 48 LYS 48 B VAL 49 n 49 VAL 49 B GLU 50 n 50 GLU 50 B MET 51 n 51 MET 51 B SER 52 n 52 SER 52 B ASP 53 n 53 ASP 53 B MET 54 n 54 MET 54 B SER 55 n 55 SER 55 B PHE 56 n 56 PHE 56 B SER 57 n 57 SER 57 B LYS 58 n 58 LYS 58 B ASP 59 n 59 ASP 59 B TRP 60 n 60 TRP 60 B SER 61 n 61 SER 61 B PHE 62 n 62 PHE 62 B TYR 63 n 63 TYR 63 B ILE 64 n 64 ILE 64 B LEU 65 n 65 LEU 65 B ALA 66 n 66 ALA 66 B HIS 67 n 67 HIS 67 B THR 68 n 68 THR 68 B GLU 69 n 69 GLU 69 B PHE 70 n 70 PHE 70 B THR 71 n 71 THR 71 B PRO 72 n 72 PRO 72 B THR 73 n 73 THR 73 B GLU 74 n 74 GLU 74 B THR 75 n 75 THR 75 B ASP 76 n 76 ASP 76 B THR 77 n 77 THR 77 B TYR 78 n 78 TYR 78 B ALA 79 n 79 ALA 79 B CYS 80 n 80 CYS 80 B ARG 81 n 81 ARG 81 B VAL 82 n 82 VAL 82 B LYS 83 n 83 LYS 83 B HIS 84 n 84 HIS 84 B ALA 85 n 85 ALA 85 B SER 86 n 86 SER 86 B MET 87 n 87 MET 87 B ALA 88 n 88 ALA 88 B GLU 89 n 89 GLU 89 B PRO 90 n 90 PRO 90 B LYS 91 n 91 LYS 91 B THR 92 n 92 THR 92 B VAL 93 n 93 VAL 93 B TYR 94 n 94 TYR 94 B TRP 95 n 95 TRP 95 B ASP 96 n 96 ASP 96 B ARG 97 n 97 ARG 97 B ASP 98 n 98 ASP 98 B MET 99 n 99 MET 99 B ARG 1 n 1 ARG 1 P GLY 2 n 2 GLY 2 P PRO 3 n 3 PRO 3 P GLY 4 n 4 GLY 4 P ARG 5 n 5 ARG 5 P ALA 6 n 6 ALA 6 P PHE 7 n 7 PHE 7 P VAL 8 n 8 VAL 8 P THR 9 n 9 THR 9 P ILE 10 n 10 ILE 10 P author_and_software_defined_assembly PISA 3 trimeric 4330 -18 18780 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A O THR 31 A O THR 31 A N VAL 28 A N VAL 28 A O ARG 21 A O ARG 21 A N VAL 12 A N VAL 12 A O HIS 3 A O HIS 3 A N VAL 103 A N VAL 103 A O GLN 96 A O GLN 96 A N ALA 117 A N ALA 117 A O ALA 125 A O ALA 125 A N THR 134 A N THR 134 A O HIS 188 A O HIS 188 A N TRP 204 A N TRP 204 A O VAL 199 A O VAL 199 A N VAL 249 A N VAL 249 A O TRP 244 A O TRP 244 A N VAL 231 A N VAL 231 A O THR 214 A O THR 214 A N GLU 262 A N GLU 262 A O CYS 259 A O CYS 259 A N LEU 272 A N LEU 272 B O ASN 21 B O ASN 21 B N PHE 70 B N PHE 70 B O GLU 36 B O GLU 36 B N LYS 83 B N LYS 83 B O CYS 80 B O CYS 80 B N VAL 93 B N VAL 93 B O SER 52 B O SER 52 B N LEU 65 B N LEU 65 1 A CB SER 2 A CB SER 2 1 Y 1 A OG SER 2 A OG SER 2 1 Y 1 A CB SER 88 A CB SER 88 1 Y 1 A OG SER 88 A OG SER 88 1 Y 1 A CB ALA 89 A CB ALA 89 1 Y 1 A CB SER 105 A CB SER 105 1 Y 1 A OG SER 105 A OG SER 105 1 Y 1 A CB ALA 117 A CB ALA 117 1 Y 1 A CB LYS 131 A CB LYS 131 1 Y 1 A CG LYS 131 A CG LYS 131 1 Y 1 A CD LYS 131 A CD LYS 131 1 Y 1 A CE LYS 131 A CE LYS 131 1 Y 1 A NZ LYS 131 A NZ LYS 131 1 Y 1 A CG LYS 186 A CG LYS 186 1 Y 1 A CD LYS 186 A CD LYS 186 1 Y 1 A CE LYS 186 A CE LYS 186 1 Y 1 A NZ LYS 186 A NZ LYS 186 1 Y 1 A CB ARG 193 A CB ARG 193 1 Y 1 A CG ARG 193 A CG ARG 193 1 Y 1 A CD ARG 193 A CD ARG 193 1 Y 1 A NE ARG 193 A NE ARG 193 1 Y 1 A CZ ARG 193 A CZ ARG 193 1 Y 1 A NH1 ARG 193 A NH1 ARG 193 1 Y 1 A NH2 ARG 193 A NH2 ARG 193 1 Y 1 A CB ARG 194 A CB ARG 194 0 Y 1 A CG ARG 194 A CG ARG 194 0 Y 1 A CD ARG 194 A CD ARG 194 0 Y 1 A NE ARG 194 A NE ARG 194 0 Y 1 A CZ ARG 194 A CZ ARG 194 0 Y 1 A NH1 ARG 194 A NH1 ARG 194 0 Y 1 A NH2 ARG 194 A NH2 ARG 194 0 Y 1 A CB GLU 196 A CB GLU 196 1 Y 1 A CG GLU 196 A CG GLU 196 1 Y 1 A CD GLU 196 A CD GLU 196 1 Y 1 A OE1 GLU 196 A OE1 GLU 196 1 Y 1 A OE2 GLU 196 A OE2 GLU 196 1 Y 1 A CB VAL 199 A CB VAL 199 1 Y 1 A CG1 VAL 199 A CG1 VAL 199 1 Y 1 A CG2 VAL 199 A CG2 VAL 199 1 Y 1 A CB LEU 224 A CB LEU 224 1 Y 1 A CG LEU 224 A CG LEU 224 1 Y 1 A CD1 LEU 224 A CD1 LEU 224 1 Y 1 A CD2 LEU 224 A CD2 LEU 224 1 Y 1 A CG LYS 253 A CG LYS 253 1 Y 1 A CD LYS 253 A CD LYS 253 1 Y 1 A CE LYS 253 A CE LYS 253 1 Y 1 A NZ LYS 253 A NZ LYS 253 1 Y 1 A CB LYS 256 A CB LYS 256 1 Y 1 A CG LYS 256 A CG LYS 256 1 Y 1 A CD LYS 256 A CD LYS 256 1 Y 1 A CE LYS 256 A CE LYS 256 1 Y 1 A NZ LYS 256 A NZ LYS 256 1 Y 1 A CB ARG 273 A CB ARG 273 1 Y 1 A CG ARG 273 A CG ARG 273 1 Y 1 A CD ARG 273 A CD ARG 273 1 Y 1 A NE ARG 273 A NE ARG 273 1 Y 1 A CZ ARG 273 A CZ ARG 273 1 Y 1 A NH1 ARG 273 A NH1 ARG 273 1 Y 1 A NH2 ARG 273 A NH2 ARG 273 1 Y 1 A CB TRP 274 A CB TRP 274 1 Y 1 A CG TRP 274 A CG TRP 274 1 Y 1 A CD1 TRP 274 A CD1 TRP 274 1 Y 1 A CD2 TRP 274 A CD2 TRP 274 1 Y 1 A NE1 TRP 274 A NE1 TRP 274 1 Y 1 A CE2 TRP 274 A CE2 TRP 274 1 Y 1 A CE3 TRP 274 A CE3 TRP 274 1 Y 1 A CZ2 TRP 274 A CZ2 TRP 274 1 Y 1 A CZ3 TRP 274 A CZ3 TRP 274 1 Y 1 A CH2 TRP 274 A CH2 TRP 274 1 Y 1 A OXT TRP 274 A OXT TRP 274 0 Y 1 B CB LYS 3 B CB LYS 3 1 Y 1 B CG LYS 3 B CG LYS 3 1 Y 1 B CD LYS 3 B CD LYS 3 1 Y 1 B CE LYS 3 B CE LYS 3 1 Y 1 B NZ LYS 3 B NZ LYS 3 1 Y 1 B CB GLN 6 B CB GLN 6 1 Y 1 B CG GLN 6 B CG GLN 6 1 Y 1 B CD GLN 6 B CD GLN 6 1 Y 1 B OE1 GLN 6 B OE1 GLN 6 1 Y 1 B NE2 GLN 6 B NE2 GLN 6 1 Y 1 B CB LYS 19 B CB LYS 19 1 Y 1 B CG LYS 19 B CG LYS 19 1 Y 1 B CD LYS 19 B CD LYS 19 1 Y 1 B CE LYS 19 B CE LYS 19 1 Y 1 B NZ LYS 19 B NZ LYS 19 1 Y 1 B CB LYS 45 B CB LYS 45 1 Y 1 B CG LYS 45 B CG LYS 45 1 Y 1 B CD LYS 45 B CD LYS 45 1 Y 1 B CE LYS 45 B CE LYS 45 1 Y 1 B NZ LYS 45 B NZ LYS 45 1 Y 1 B CB LYS 48 B CB LYS 48 1 Y 1 B CG LYS 48 B CG LYS 48 1 Y 1 B CD LYS 48 B CD LYS 48 1 Y 1 B CE LYS 48 B CE LYS 48 1 Y 1 B NZ LYS 48 B NZ LYS 48 1 Y 1 B CB SER 57 B CB SER 57 1 Y 1 B OG SER 57 B OG SER 57 1 Y 1 B CB GLU 74 B CB GLU 74 1 Y 1 B CG GLU 74 B CG GLU 74 1 Y 1 B CD GLU 74 B CD GLU 74 1 Y 1 B OE1 GLU 74 B OE1 GLU 74 1 Y 1 B OE2 GLU 74 B OE2 GLU 74 1 Y 1 A SER 2 -139.77 -72.96 1 A SER 13 -66.29 99.26 1 A ASP 29 55.93 -130.86 1 A ASN 30 -104.72 51.80 1 A GLU 41 -52.79 -76.82 1 A PRO 43 -85.06 49.23 1 A ARG 48 -84.67 48.04 1 A ALA 49 175.33 147.13 1 A GLU 53 -45.70 -19.01 1 A ASN 86 57.59 13.38 1 A TRP 114 -161.25 88.32 1 A ASP 119 78.38 -73.46 1 A TYR 123 -104.22 -74.61 1 A ASN 127 -52.99 174.15 1 A ASP 129 -58.13 -3.61 1 A LEU 179 -81.00 -117.13 1 A LEU 180 10.06 -55.16 1 A ALA 181 -18.31 80.80 1 A LYS 186 -115.65 66.91 1 A ALA 187 -58.19 173.68 1 A HIS 188 163.55 137.99 1 A PRO 195 -69.21 -123.71 1 A GLU 196 31.09 33.18 1 A TYR 209 -175.97 133.10 1 A GLU 212 -39.24 126.26 1 A THR 225 -127.57 -67.95 1 A GLN 226 -64.12 67.18 1 A GLU 227 176.70 -26.04 1 A THR 233 -61.20 94.09 1 A LYS 243 162.44 172.65 1 A LEU 251 -50.54 97.21 1 A GLN 254 10.41 -64.45 1 A ARG 273 -173.43 -177.71 1 B GLN 2 -162.20 103.74 1 B PRO 20 -42.57 163.44 1 B ASN 21 -172.35 -167.85 1 B TYR 26 -44.67 107.02 1 B GLN 29 38.96 28.53 1 B PRO 47 -44.97 -71.71 1 B VAL 49 -64.70 75.73 1 B ASP 53 103.72 -133.81 1 B MET 54 95.49 79.10 1 B SER 55 -156.12 -158.01 1 B TRP 60 70.03 -27.11 1 B HIS 67 -164.78 109.37 1 B ASP 76 -33.72 110.85 1 B ASP 98 -52.16 98.35 1 P ALA 6 -69.95 40.21 1 P THR 9 -57.89 -167.53 PARHCSDX.PRO TOPHCSDX.PRO 0.337 0.229 0.229 3.1 8.0 641 7863 7.0 86.4 RANDOM 0 1 THROUGHOUT 2.0 MOLECULAR REPLACEMENT PDB ENTRY 1VAD 3.1 8.0 4 3051 0 0 3047 0.010 1.72 23.9 1.35 0.476 0.309 3.2 64 7267 10 7.0 79.8 3.1 1DDH 33412 0.081 0.081 1 12.7 3.6 86.8 0.389 3.1 3.2 2.4 0.389 75.0 data reduction DENZO data scaling SCALEPACK phasing AMoRE refinement X-PLOR 3.1 MHC CLASS I H-2DD HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND AN IMMUNODOMINANT PEPTIDE P18-I10 FROM THE HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120 1 N N 2 N N 3 N N 4 N N A TRP 51 A TRP 51 HELX_P A GLN 54 A GLN 54 5 1 4 A PRO 57 A PRO 57 HELX_P A TYR 85 A TYR 85 1 2 29 A MET 138 A MET 138 HELX_P A GLN 149 A GLN 149 1 3 12 A ALA 152 A ALA 152 HELX_P A GLU 161 A GLU 161 1 4 10 A GLU 163 A GLU 163 HELX_P A LYS 173 A LYS 173 1 5 11 A GLN 254 A GLN 254 HELX_P A LYS 256 A LYS 256 5 6 3 disulf 2.034 A CYS 101 A SG CYS 101 1_555 A CYS 164 A SG CYS 164 1_555 disulf 2.034 A CYS 203 A SG CYS 203 1_555 A CYS 259 A SG CYS 259 1_555 disulf 2.020 B CYS 25 B SG CYS 25 1_555 B CYS 80 B SG CYS 80 1_555 COMPLEX (HISTOCOMPATIBILITY/ANTIGEN) COMPLEX (HISTOCOMPATIBILITY-ANTIGEN), HISTOCOMPATIBILITY ANTIGEN, CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX, MHC I, COMPLEX (HISTOCOMPATIBILITY-ANTIGEN) complex A TYR 209 A TYR 209 1 A PRO 210 A PRO 210 -0.11 B HIS 31 B HIS 31 1 B PRO 32 B PRO 32 1.69 HA12_MOUSE UNP 1 26 P01900 B2MG_MOUSE UNP 2 22 P01887 ENV_HV1B8 UNP 3 311 P04582 26 298 1DDH 2 274 P01900 A 1 2 274 22 119 1DDH 2 99 P01887 B 2 2 99 311 320 1DDH 1 10 P04582 P 3 1 10 1 LYS conflict ASN 68 1DDH A P01900 UNP 92 68 1 ARG conflict ALA 181 1DDH A P01900 UNP 205 181 1 ASP conflict GLU 212 1DDH A P01900 UNP 236 212 1 GLU conflict GLN 254 1DDH A P01900 UNP 278 254 2 ASP conflict ALA 85 1DDH B P01887 UNP 105 85 5 2 4 3 2 3 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A THR 31 A THR 31 A ASP 37 A ASP 37 A ARG 21 A ARG 21 A VAL 28 A VAL 28 A HIS 3 A HIS 3 A SER 13 A SER 13 A HIS 93 A HIS 93 A VAL 103 A VAL 103 A LEU 109 A LEU 109 A TYR 118 A TYR 118 A ILE 124 A ILE 124 A LEU 126 A LEU 126 A TRP 133 A TRP 133 A ALA 135 A ALA 135 A HIS 188 A HIS 188 A HIS 192 A HIS 192 A ASP 198 A ASP 198 A TRP 204 A TRP 204 A TRP 244 A TRP 244 A PRO 250 A PRO 250 A MET 228 A MET 228 A VAL 231 A VAL 231 A THR 214 A THR 214 A LEU 219 A LEU 219 A TYR 257 A TYR 257 A GLU 262 A GLU 262 A LEU 270 A LEU 270 A LEU 272 A LEU 272 B PRO 20 B PRO 20 B ASN 24 B ASN 24 B HIS 67 B HIS 67 B THR 71 B THR 71 B GLU 36 B GLU 36 B LYS 41 B LYS 41 B TYR 78 B TYR 78 B LYS 83 B LYS 83 B LYS 91 B LYS 91 B TYR 94 B TYR 94 B MET 51 B MET 51 B PHE 56 B PHE 56 B PHE 62 B PHE 62 B ALA 66 B ALA 66 19 P 21 21 21