0.015734 0.000000 0.000000 0.000000 0.014938 0.000000 0.000000 0.000000 0.011360 0.00000 0.00000 0.00000 Kwon, Y.D. Kwong, P.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 63.556 66.944 88.029 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 C8 H18 N2 O4 S 238.305 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HEPES non-polymer 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 C8 H15 N O6 221.208 2-acetamido-2-deoxy-beta-D-glucopyranose D-saccharide, beta 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 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 109 5663 5668 10.1073/pnas.1112391109 22451932 Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops. 2012 100 1 IMAGE PLATE 2010-07-16 MAR scanner 300 mm plate SINGLE WAVELENGTH M x-ray 1 1 1.0 22-BM APS 1 SYNCHROTRON APS BEAMLINE 22-BM 39211.434 HIV-1 clade A/E 93TH057 gp120 1 man polymer 221.208 2-acetamido-2-deoxy-beta-D-glucopyranose 10 man non-polymer 238.305 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID 1 syn non-polymer 18.015 water 148 nat water no no VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLT GGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSEN LTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM HHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGG ANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLT GGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSEN LTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM HHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGG ANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE A 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 HIV-1 sample HIV-1 env 11676 Human immunodeficiency virus 1 HEK 293 9606 HOMO SAPIENS plasmid pVRC8400 1 2.39 48.49 VAPOR DIFFUSION, HANGING DROP 7.5 14% PEG 1500, 12% PEG 400, 0.1M HEPES, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5 293 software chem_comp entity pdbx_chem_comp_identifier pdbx_entity_nonpoly struct_conn struct_site struct_site_gen repository Initial release Carbohydrate remediation repository Remediation Database references Refinement description Data collection Derived calculations Structure summary 1 0 2012-04-04 1 1 2012-05-23 1 2 2017-11-08 1 3 2020-07-29 _chem_comp.name _chem_comp.type _entity.pdbx_description _pdbx_entity_nonpoly.name _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_role _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id DGlcpNAcb N-acetyl-b-D-glucopyranosamine b-D-GlcpNAc GlcNAc RCSB Y RCSB 2011-08-17 REL REL NAG 2-acetamido-2-deoxy-beta-D-glucopyranose EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HOH water NAG 734 2 NAG NAG 734 A NAG 741 2 NAG NAG 741 A NAG 762 2 NAG NAG 762 A NAG 776 2 NAG NAG 776 A NAG 789 2 NAG NAG 789 A NAG 795 2 NAG NAG 795 A NAG 834 2 NAG NAG 834 A NAG 886 2 NAG NAG 886 A NAG 892 2 NAG NAG 892 A NAG 948 2 NAG NAG 948 A EPE 1 3 EPE EPE 1 A HOH 2 4 HOH HOH 2 A HOH 3 4 HOH HOH 3 A HOH 4 4 HOH HOH 4 A HOH 5 4 HOH HOH 5 A HOH 6 4 HOH HOH 6 A HOH 7 4 HOH HOH 7 A HOH 8 4 HOH HOH 8 A HOH 9 4 HOH HOH 9 A HOH 10 4 HOH HOH 10 A HOH 11 4 HOH HOH 11 A HOH 12 4 HOH HOH 12 A HOH 13 4 HOH HOH 13 A HOH 14 4 HOH HOH 14 A HOH 15 4 HOH HOH 15 A HOH 16 4 HOH HOH 16 A HOH 17 4 HOH HOH 17 A HOH 18 4 HOH HOH 18 A HOH 19 4 HOH HOH 19 A HOH 20 4 HOH HOH 20 A HOH 21 4 HOH HOH 21 A HOH 22 4 HOH HOH 22 A HOH 23 4 HOH HOH 23 A HOH 24 4 HOH HOH 24 A HOH 25 4 HOH HOH 25 A HOH 26 4 HOH HOH 26 A HOH 27 4 HOH HOH 27 A HOH 28 4 HOH HOH 28 A HOH 29 4 HOH HOH 29 A HOH 30 4 HOH HOH 30 A HOH 31 4 HOH HOH 31 A HOH 32 4 HOH HOH 32 A HOH 33 4 HOH HOH 33 A HOH 34 4 HOH HOH 34 A HOH 35 4 HOH HOH 35 A HOH 36 4 HOH HOH 36 A HOH 37 4 HOH HOH 37 A HOH 38 4 HOH HOH 38 A HOH 39 4 HOH HOH 39 A HOH 40 4 HOH HOH 40 A HOH 41 4 HOH HOH 41 A HOH 42 4 HOH HOH 42 A HOH 43 4 HOH HOH 43 A HOH 125 4 HOH HOH 125 A HOH 126 4 HOH HOH 126 A HOH 127 4 HOH HOH 127 A HOH 128 4 HOH HOH 128 A HOH 129 4 HOH HOH 129 A HOH 130 4 HOH HOH 130 A HOH 131 4 HOH HOH 131 A HOH 132 4 HOH HOH 132 A HOH 133 4 HOH HOH 133 A HOH 134 4 HOH HOH 134 A HOH 135 4 HOH HOH 135 A HOH 136 4 HOH HOH 136 A HOH 137 4 HOH HOH 137 A HOH 138 4 HOH HOH 138 A HOH 139 4 HOH HOH 139 A HOH 140 4 HOH HOH 140 A HOH 141 4 HOH HOH 141 A HOH 142 4 HOH HOH 142 A HOH 143 4 HOH HOH 143 A HOH 144 4 HOH HOH 144 A HOH 145 4 HOH HOH 145 A HOH 146 4 HOH HOH 146 A HOH 147 4 HOH HOH 147 A HOH 148 4 HOH HOH 148 A HOH 1 4 HOH HOH 493 A HOH 44 4 HOH HOH 494 A HOH 45 4 HOH HOH 495 A HOH 46 4 HOH HOH 496 A HOH 47 4 HOH HOH 497 A HOH 48 4 HOH HOH 498 A HOH 49 4 HOH HOH 499 A HOH 50 4 HOH HOH 500 A HOH 51 4 HOH HOH 501 A HOH 52 4 HOH HOH 502 A HOH 53 4 HOH HOH 503 A HOH 54 4 HOH HOH 504 A HOH 55 4 HOH HOH 505 A HOH 56 4 HOH HOH 506 A HOH 57 4 HOH HOH 507 A HOH 58 4 HOH HOH 508 A HOH 59 4 HOH HOH 509 A HOH 60 4 HOH HOH 510 A HOH 61 4 HOH HOH 511 A HOH 62 4 HOH HOH 512 A HOH 63 4 HOH HOH 513 A HOH 64 4 HOH HOH 514 A HOH 65 4 HOH HOH 515 A HOH 66 4 HOH HOH 516 A HOH 67 4 HOH HOH 517 A HOH 68 4 HOH HOH 518 A HOH 69 4 HOH HOH 519 A HOH 70 4 HOH HOH 520 A HOH 71 4 HOH HOH 521 A HOH 72 4 HOH HOH 522 A HOH 73 4 HOH HOH 523 A HOH 74 4 HOH HOH 524 A HOH 75 4 HOH HOH 525 A HOH 76 4 HOH HOH 526 A HOH 77 4 HOH HOH 527 A HOH 78 4 HOH HOH 528 A HOH 79 4 HOH HOH 529 A HOH 80 4 HOH HOH 530 A HOH 81 4 HOH HOH 531 A HOH 82 4 HOH HOH 532 A HOH 83 4 HOH HOH 533 A HOH 84 4 HOH HOH 534 A HOH 85 4 HOH HOH 535 A HOH 86 4 HOH HOH 536 A HOH 87 4 HOH HOH 537 A HOH 88 4 HOH HOH 538 A HOH 89 4 HOH HOH 539 A HOH 90 4 HOH HOH 540 A HOH 91 4 HOH HOH 541 A HOH 92 4 HOH HOH 542 A HOH 93 4 HOH HOH 543 A HOH 94 4 HOH HOH 544 A HOH 95 4 HOH HOH 545 A HOH 96 4 HOH HOH 546 A HOH 97 4 HOH HOH 547 A HOH 98 4 HOH HOH 548 A HOH 99 4 HOH HOH 549 A HOH 100 4 HOH HOH 550 A HOH 101 4 HOH HOH 551 A HOH 102 4 HOH HOH 552 A HOH 103 4 HOH HOH 553 A HOH 104 4 HOH HOH 554 A HOH 105 4 HOH HOH 555 A HOH 106 4 HOH HOH 556 A HOH 107 4 HOH HOH 557 A HOH 108 4 HOH HOH 558 A HOH 109 4 HOH HOH 559 A HOH 110 4 HOH HOH 560 A HOH 111 4 HOH HOH 561 A HOH 112 4 HOH HOH 562 A HOH 113 4 HOH HOH 563 A HOH 114 4 HOH HOH 564 A HOH 115 4 HOH HOH 565 A HOH 116 4 HOH HOH 566 A HOH 117 4 HOH HOH 567 A HOH 118 4 HOH HOH 568 A HOH 119 4 HOH HOH 569 A HOH 120 4 HOH HOH 570 A HOH 121 4 HOH HOH 571 A HOH 122 4 HOH HOH 572 A HOH 123 4 HOH HOH 573 A HOH 124 4 HOH HOH 574 A VAL 44 n 1 VAL 44 A TRP 45 n 2 TRP 45 A LYS 46 n 3 LYS 46 A ASP 47 n 4 ASP 47 A ALA 48 n 5 ALA 48 A ASP 49 n 6 ASP 49 A THR 50 n 7 THR 50 A THR 51 n 8 THR 51 A LEU 52 n 9 LEU 52 A PHE 53 n 10 PHE 53 A CYS 54 n 11 CYS 54 A ALA 55 n 12 ALA 55 A SER 56 n 13 SER 56 A ASP 57 n 14 ASP 57 A ALA 58 n 15 ALA 58 A LYS 59 n 16 LYS 59 A ALA 60 n 17 ALA 60 A HIS 61 n 18 HIS 61 A GLU 62 n 19 GLU 62 A THR 63 n 20 THR 63 A GLU 64 n 21 GLU 64 A VAL 65 n 22 VAL 65 A HIS 66 n 23 HIS 66 A ASN 67 n 24 ASN 67 A VAL 68 n 25 VAL 68 A TRP 69 n 26 TRP 69 A ALA 70 n 27 ALA 70 A THR 71 n 28 THR 71 A HIS 72 n 29 HIS 72 A ALA 73 n 30 ALA 73 A CYS 74 n 31 CYS 74 A VAL 75 n 32 VAL 75 A PRO 76 n 33 PRO 76 A THR 77 n 34 THR 77 A ASP 78 n 35 ASP 78 A PRO 79 n 36 PRO 79 A ASN 80 n 37 ASN 80 A PRO 81 n 38 PRO 81 A GLN 82 n 39 GLN 82 A GLU 83 n 40 GLU 83 A ILE 84 n 41 ILE 84 A HIS 85 n 42 HIS 85 A LEU 86 n 43 LEU 86 A GLU 87 n 44 GLU 87 A ASN 88 n 45 ASN 88 A VAL 89 n 46 VAL 89 A THR 90 n 47 THR 90 A GLU 91 n 48 GLU 91 A ASN 92 n 49 ASN 92 A PHE 93 n 50 PHE 93 A ASN 94 n 51 ASN 94 A MET 95 n 52 MET 95 A TRP 96 n 53 TRP 96 A LYS 97 n 54 LYS 97 A ASN 98 n 55 ASN 98 A ASN 99 n 56 ASN 99 A MET 100 n 57 MET 100 A VAL 101 n 58 VAL 101 A GLU 102 n 59 GLU 102 A GLN 103 n 60 GLN 103 A MET 104 n 61 MET 104 A GLN 105 n 62 GLN 105 A GLU 106 n 63 GLU 106 A ASP 107 n 64 ASP 107 A VAL 108 n 65 VAL 108 A ILE 109 n 66 ILE 109 A SER 110 n 67 SER 110 A LEU 111 n 68 LEU 111 A TRP 112 n 69 TRP 112 A ASP 113 n 70 ASP 113 A GLN 114 n 71 GLN 114 A SER 115 n 72 SER 115 A LEU 116 n 73 LEU 116 A GLN 117 n 74 GLN 117 A PRO 118 n 75 PRO 118 A CYS 119 n 76 CYS 119 A VAL 120 n 77 VAL 120 A LYS 121 n 78 LYS 121 A LEU 122 n 79 LEU 122 A THR 123 n 80 THR 123 A GLY 124 n 81 GLY 124 A GLY 198 n 82 GLY 198 A SER 199 n 83 SER 199 A VAL 200 n 84 VAL 200 A ILE 201 n 85 ILE 201 A LYS 202 n 86 LYS 202 A GLN 203 n 87 GLN 203 A ALA 204 n 88 ALA 204 A CYS 205 n 89 CYS 205 A PRO 206 n 90 PRO 206 A LYS 207 n 91 LYS 207 A ILE 208 n 92 ILE 208 A SER 209 n 93 SER 209 A PHE 210 n 94 PHE 210 A ASP 211 n 95 ASP 211 A PRO 212 n 96 PRO 212 A ILE 213 n 97 ILE 213 A PRO 214 n 98 PRO 214 A ILE 215 n 99 ILE 215 A HIS 216 n 100 HIS 216 A TYR 217 n 101 TYR 217 A CYS 218 n 102 CYS 218 A THR 219 n 103 THR 219 A PRO 220 n 104 PRO 220 A ALA 221 n 105 ALA 221 A GLY 222 n 106 GLY 222 A TYR 223 n 107 TYR 223 A VAL 224 n 108 VAL 224 A ILE 225 n 109 ILE 225 A LEU 226 n 110 LEU 226 A LYS 227 n 111 LYS 227 A CYS 228 n 112 CYS 228 A ASN 229 n 113 ASN 229 A ASP 230 n 114 ASP 230 A LYS 231 n 115 LYS 231 A ASN 232 n 116 ASN 232 A PHE 233 n 117 PHE 233 A ASN 234 n 118 ASN 234 A GLY 235 n 119 GLY 235 A THR 236 n 120 THR 236 A GLY 237 n 121 GLY 237 A PRO 238 n 122 PRO 238 A CYS 239 n 123 CYS 239 A LYS 240 n 124 LYS 240 A ASN 241 n 125 ASN 241 A VAL 242 n 126 VAL 242 A SER 243 n 127 SER 243 A SER 244 n 128 SER 244 A VAL 245 n 129 VAL 245 A GLN 246 n 130 GLN 246 A CYS 247 n 131 CYS 247 A THR 248 n 132 THR 248 A HIS 249 n 133 HIS 249 A GLY 250 n 134 GLY 250 A ILE 251 n 135 ILE 251 A LYS 252 n 136 LYS 252 A PRO 253 n 137 PRO 253 A VAL 254 n 138 VAL 254 A VAL 255 n 139 VAL 255 A SER 256 n 140 SER 256 A THR 257 n 141 THR 257 A GLN 258 n 142 GLN 258 A LEU 259 n 143 LEU 259 A LEU 260 n 144 LEU 260 A LEU 261 n 145 LEU 261 A ASN 262 n 146 ASN 262 A GLY 263 n 147 GLY 263 A SER 264 n 148 SER 264 A LEU 265 n 149 LEU 265 A ALA 266 n 150 ALA 266 A GLU 267 n 151 GLU 267 A GLU 268 n 152 GLU 268 A GLU 269 n 153 GLU 269 A ILE 270 n 154 ILE 270 A ILE 271 n 155 ILE 271 A ILE 272 n 156 ILE 272 A ARG 273 n 157 ARG 273 A SER 274 n 158 SER 274 A GLU 275 n 159 GLU 275 A ASN 276 n 160 ASN 276 A LEU 277 n 161 LEU 277 A THR 278 n 162 THR 278 A ASN 279 n 163 ASN 279 A ASN 280 n 164 ASN 280 A ALA 281 n 165 ALA 281 A LYS 282 n 166 LYS 282 A THR 283 n 167 THR 283 A ILE 284 n 168 ILE 284 A ILE 285 n 169 ILE 285 A VAL 286 n 170 VAL 286 A HIS 287 n 171 HIS 287 A LEU 288 n 172 LEU 288 A ASN 289 n 173 ASN 289 A LYS 290 n 174 LYS 290 A SER 291 n 175 SER 291 A VAL 292 n 176 VAL 292 A GLU 293 n 177 GLU 293 A ILE 294 n 178 ILE 294 A ASN 295 n 179 ASN 295 A CYS 296 n 180 CYS 296 A THR 297 n 181 THR 297 A ARG 298 n 182 ARG 298 A PRO 299 n 183 PRO 299 A SER 300 n 184 SER 300 A ASN 301 n 185 ASN 301 A n 186 318 A n 187 319 A n 188 320 A n 189 321 A n 190 322 A n 191 323 A GLY 324 n 192 GLY 324 A ASP 325 n 193 ASP 325 A ILE 326 n 194 ILE 326 A ARG 327 n 195 ARG 327 A LYS 328 n 196 LYS 328 A ALA 329 n 197 ALA 329 A TYR 330 n 198 TYR 330 A CYS 331 n 199 CYS 331 A GLU 332 n 200 GLU 332 A ILE 333 n 201 ILE 333 A ASN 334 n 202 ASN 334 A GLY 335 n 203 GLY 335 A THR 336 n 204 THR 336 A LYS 337 n 205 LYS 337 A TRP 338 n 206 TRP 338 A ASN 339 n 207 ASN 339 A LYS 340 n 208 LYS 340 A VAL 341 n 209 VAL 341 A LEU 342 n 210 LEU 342 A LYS 343 n 211 LYS 343 A GLN 344 n 212 GLN 344 A VAL 345 n 213 VAL 345 A THR 346 n 214 THR 346 A GLU 347 n 215 GLU 347 A LYS 348 n 216 LYS 348 A LEU 349 n 217 LEU 349 A LYS 350 n 218 LYS 350 A GLU 351 n 219 GLU 351 A HIS 352 n 220 HIS 352 A PHE 353 n 221 PHE 353 A ASN 354 n 222 ASN 354 A ASN 355 n 223 ASN 355 A LYS 357 n 224 LYS 357 A THR 358 n 225 THR 358 A ILE 359 n 226 ILE 359 A ILE 360 n 227 ILE 360 A PHE 361 n 228 PHE 361 A GLN 362 n 229 GLN 362 A PRO 363 n 230 PRO 363 A PRO 364 n 231 PRO 364 A SER 365 n 232 SER 365 A GLY 366 n 233 GLY 366 A GLY 367 n 234 GLY 367 A ASP 368 n 235 ASP 368 A LEU 369 n 236 LEU 369 A GLU 370 n 237 GLU 370 A ILE 371 n 238 ILE 371 A THR 372 n 239 THR 372 A MET 373 n 240 MET 373 A HIS 374 n 241 HIS 374 A HIS 375 n 242 HIS 375 A PHE 376 n 243 PHE 376 A ASN 377 n 244 ASN 377 A CYS 378 n 245 CYS 378 A ARG 379 n 246 ARG 379 A GLY 380 n 247 GLY 380 A GLU 381 n 248 GLU 381 A PHE 382 n 249 PHE 382 A PHE 383 n 250 PHE 383 A TYR 384 n 251 TYR 384 A CYS 385 n 252 CYS 385 A ASN 386 n 253 ASN 386 A THR 387 n 254 THR 387 A THR 388 n 255 THR 388 A GLN 389 n 256 GLN 389 A LEU 390 n 257 LEU 390 A PHE 391 n 258 PHE 391 A ASN 392 n 259 ASN 392 A ASN 393 n 260 ASN 393 A THR 394 n 261 THR 394 A CYS 395 n 262 CYS 395 A ILE 396 n 263 ILE 396 A n 264 403 A n 265 404 A n 266 405 A n 267 406 A n 268 407 A LYS 408 n 269 LYS 408 A GLY 409 n 270 GLY 409 A CYS 410 n 271 CYS 410 A ASN 411 n 272 ASN 411 A GLY 412 n 273 GLY 412 A THR 413 n 274 THR 413 A ILE 414 n 275 ILE 414 A THR 415 n 276 THR 415 A LEU 416 n 277 LEU 416 A PRO 417 n 278 PRO 417 A CYS 418 n 279 CYS 418 A LYS 419 n 280 LYS 419 A ILE 420 n 281 ILE 420 A LYS 421 n 282 LYS 421 A GLN 422 n 283 GLN 422 A ILE 423 n 284 ILE 423 A ILE 424 n 285 ILE 424 A ASN 425 n 286 ASN 425 A MET 426 n 287 MET 426 A TRP 427 n 288 TRP 427 A GLN 428 n 289 GLN 428 A GLY 429 n 290 GLY 429 A THR 430 n 291 THR 430 A GLY 431 n 292 GLY 431 A GLN 432 n 293 GLN 432 A ALA 433 n 294 ALA 433 A MET 434 n 295 MET 434 A TYR 435 n 296 TYR 435 A ALA 436 n 297 ALA 436 A PRO 437 n 298 PRO 437 A PRO 438 n 299 PRO 438 A ILE 439 n 300 ILE 439 A ASP 440 n 301 ASP 440 A GLY 441 n 302 GLY 441 A LYS 442 n 303 LYS 442 A ILE 443 n 304 ILE 443 A ASN 444 n 305 ASN 444 A CYS 445 n 306 CYS 445 A VAL 446 n 307 VAL 446 A SER 447 n 308 SER 447 A ASN 448 n 309 ASN 448 A ILE 449 n 310 ILE 449 A THR 450 n 311 THR 450 A GLY 451 n 312 GLY 451 A ILE 452 n 313 ILE 452 A LEU 453 n 314 LEU 453 A LEU 454 n 315 LEU 454 A THR 455 n 316 THR 455 A ARG 456 n 317 ARG 456 A ASP 457 n 318 ASP 457 A GLY 458 n 319 GLY 458 A GLY 459 n 320 GLY 459 A ALA 460 n 321 ALA 460 A ASN 461 n 322 ASN 461 A ASN 462 n 323 ASN 462 A THR 463 n 324 THR 463 A SER 464 n 325 SER 464 A ASN 465 n 326 ASN 465 A GLU 466 n 327 GLU 466 A THR 467 n 328 THR 467 A PHE 468 n 329 PHE 468 A ARG 469 n 330 ARG 469 A PRO 470 n 331 PRO 470 A GLY 471 n 332 GLY 471 A GLY 472 n 333 GLY 472 A GLY 473 n 334 GLY 473 A ASN 474 n 335 ASN 474 A ILE 475 n 336 ILE 475 A LYS 476 n 337 LYS 476 A ASP 477 n 338 ASP 477 A ASN 478 n 339 ASN 478 A TRP 479 n 340 TRP 479 A ARG 480 n 341 ARG 480 A SER 481 n 342 SER 481 A GLU 482 n 343 GLU 482 A LEU 483 n 344 LEU 483 A TYR 484 n 345 TYR 484 A LYS 485 n 346 LYS 485 A TYR 486 n 347 TYR 486 A LYS 487 n 348 LYS 487 A VAL 488 n 349 VAL 488 A VAL 489 n 350 VAL 489 A GLN 490 n 351 GLN 490 A ILE 491 n 352 ILE 491 A GLU 492 n 353 GLU 492 A 1.3719 0.0160 -0.9221 0.8971 -0.5505 0.8850 -0.0685 -0.1073 0.3159 -0.1386 0.0355 -0.0473 -0.4479 0.3098 0.0401 0.4241 -0.0748 -0.0077 0.3251 0.0066 0.2948 refined 15.7912 7.5291 -18.3549 X-RAY DIFFRACTION 1.3780 0.6429 0.7281 2.4082 0.9575 2.4516 -0.1086 -0.1682 0.1367 0.0236 -0.0019 0.1441 -0.1841 0.0563 0.0820 0.2575 -0.0231 0.0274 0.2436 0.0108 0.2280 refined 11.6296 -1.6387 -13.8940 X-RAY DIFFRACTION 1.8624 0.3582 1.2056 2.1698 0.5581 2.9239 0.0584 0.1011 -0.2977 0.1776 0.1187 -0.2488 0.3329 0.2811 -0.1788 0.2850 0.0524 0.0071 0.2674 -0.0256 0.3199 refined 15.9172 -21.2629 -15.1480 X-RAY DIFFRACTION 0.5689 -0.4296 0.0995 1.4921 -0.4937 0.2340 -0.1333 -0.3578 0.0285 0.2787 0.1294 -0.0060 -0.0038 0.1200 -0.0069 0.2943 -0.0358 -0.0195 0.3541 -0.0152 0.2599 refined 16.6589 0.2471 -7.9503 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain A and resi 44:89 X-RAY DIFFRACTION 2 chain A and resi 90:254 X-RAY DIFFRACTION 3 chain A and resi 255:474 X-RAY DIFFRACTION 4 chain A and resi 475:492 author_and_software_defined_assembly PISA 1 monomeric A ASN 234 GLYCOSYLATION SITE A ASN 118 ASN A ASN 334 GLYCOSYLATION SITE A ASN 202 ASN A ASN 386 GLYCOSYLATION SITE A ASN 253 ASN A ASN 448 GLYCOSYLATION SITE A ASN 309 ASN A ASN 289 GLYCOSYLATION SITE A ASN 173 ASN A ASN 241 GLYCOSYLATION SITE A ASN 125 ASN A ASN 262 GLYCOSYLATION SITE A ASN 146 ASN A ASN 295 GLYCOSYLATION SITE A ASN 179 ASN A ASN 392 GLYCOSYLATION SITE A ASN 259 ASN A ASN 276 GLYCOSYLATION SITE A ASN 160 ASN 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 N LYS 46 A N LYS 3 A O GLN 490 A O GLN 351 A O LYS 487 A O LYS 348 A N LEU 226 A N LEU 110 A N LYS 227 A N LYS 111 A O SER 243 A O SER 127 A O SER 244 A O SER 128 A N ILE 84 A N ILE 41 A O VAL 75 A O VAL 32 A N CYS 54 A N CYS 11 A N ALA 55 A N ALA 12 A O HIS 216 A O HIS 100 A N PHE 93 A N PHE 50 A O GLY 237 A O GLY 121 A O SER 199 A O SER 83 A N THR 123 A N THR 80 A N LEU 122 A N LEU 79 A O GLN 432 A O GLN 293 A O ALA 433 A O ALA 294 A N ILE 424 A N ILE 285 A N LEU 260 A N LEU 144 A O THR 450 A O THR 311 A O ILE 452 A O ILE 313 A N VAL 286 A N VAL 170 A O PHE 468 A O PHE 329 A N ILE 360 A N ILE 227 A N ILE 271 A N ILE 155 A O HIS 287 A O HIS 171 A N VAL 286 A N VAL 170 A O ILE 452 A O ILE 313 A N ILE 333 A N ILE 201 A O ILE 414 A O ILE 275 A O LYS 419 A O LYS 280 A N TYR 384 A N TYR 251 A O PHE 383 A O PHE 250 A N PHE 376 A N PHE 243 1 A GLY 318 A GLY 186 1 Y 1 A GLY 319 A GLY 187 1 Y 1 A SER 320 A SER 188 1 Y 1 A GLY 321 A GLY 189 1 Y 1 A SER 322 A SER 190 1 Y 1 A GLY 323 A GLY 191 1 Y 1 A GLY 403 A GLY 264 1 Y 1 A ASN 404 A ASN 265 1 Y 1 A GLU 405 A GLU 266 1 Y 1 A THR 406 A THR 267 1 Y 1 A MET 407 A MET 268 1 Y 1 A A O O HOH HOH 565 566 1.92 1 A A O O HOH HOH 135 567 2.00 1 A A ND2 O5 ASN NAG 234 734 2.02 1 A ASN 88 35.01 39.43 1 A LEU 116 -112.54 66.07 1 A ASP 211 -168.87 107.73 1 A GLN 258 69.17 -59.25 1 A GLU 268 -131.94 -99.50 1 A ASN 276 -173.00 94.68 1 A PHE 391 -108.48 61.19 1 A ASN 474 -178.92 112.89 10.7220 -0.0000 -0.0000 -4.9969 -0.0000 -5.7251 0.2307 0.1890 0.1910 1.9 24.571 1437 31824 29250 4.91 91.91 1.000 1.000 0.24 1 0.11 MOLECULAR REPLACEMENT 23.44 0.90 1.11 ML FLAT BULK SOLVENT MODEL 36.441 0.329 1.9 24.571 148 2980 155 0 2677 0.007 2921 1.198 3960 15.937 1105 0.069 462 0.004 492 0.2307 0.2349 1.9343 83 1817 61.00 0.2760 0.2176 2.0117 152 2475 84.00 0.3130 0.2093 2.1032 166 2717 92.00 0.2610 0.2029 2.2140 144 2814 94.00 0.2560 0.1970 2.3526 141 2858 95.00 0.2440 0.2037 2.5341 158 2896 97.00 0.2692 0.1966 2.7888 152 2953 98.00 0.2095 0.1973 3.1916 142 3038 99.00 0.2326 0.1776 4.0182 145 3055 99.00 0.1972 0.1747 24.5735 154 3190 99.00 1.9 50 3TGT 32465 30907 0.0 0.0 0.084 0.074 1 38.5 6.8 95.2 0.615 1.90 1.93 2.1 0.555 1 5.5 86.5 0.498 1.93 1.97 2.7 0.452 1 5.8 89.9 0.479 1.97 2.01 3.1 0.416 1 6.0 95.2 0.419 2.01 2.05 3.7 0.368 1 6.4 97.8 0.377 2.05 2.09 4.9 0.339 1 6.7 99.5 0.327 2.09 2.14 6.3 0.269 1 6.9 99.8 0.296 2.14 2.19 7.3 0.265 1 7.1 100.0 0.257 2.19 2.25 9.6 0.226 1 7.2 100.0 0.219 2.25 2.32 11.9 0.197 1 7.3 100.0 0.190 2.32 2.39 15.5 0.172 1 7.3 99.9 0.171 2.39 2.48 16.5 0.155 1 7.2 100.0 0.144 2.48 2.58 20.9 0.137 1 7.2 100.0 0.129 2.58 2.70 24.6 0.126 1 7.2 100.0 0.115 2.70 2.84 28.7 0.116 1 7.1 99.9 0.101 2.84 3.02 34.5 0.103 1 7.1 100.0 0.091 3.02 3.25 41.9 0.093 1 6.9 99.9 0.085 3.25 3.58 46.2 0.090 1 6.6 100.0 0.075 3.58 4.09 51.3 0.081 1 6.3 99.9 0.067 4.09 5.16 57.3 0.075 1 6.6 99.9 0.053 5.16 50.00 57.9 0.062 1 6.4 98.1 refinement Paul D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package 1.6.1_357 data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 data reduction DENZO data scaling SCALEPACK HIV-1 clade A/E 93TH057 gp120 Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 gp120 core 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N 4 N N A GLU 64 A GLU 21 HELX_P A CYS 74 A CYS 31 1 1 11 A ASN 98 A ASN 55 HELX_P A LEU 116 A LEU 73 1 2 19 A GLY 335 A GLY 203 HELX_P A PHE 353 A PHE 221 1 3 19 A ASP 368 A ASP 235 HELX_P A MET 373 A MET 240 1 4 6 A THR 387 A THR 254 HELX_P A ILE 396 A ILE 263 5 5 10 A GLY 459 A GLY 320 HELX_P A THR 463 A THR 324 5 6 5 A ASN 474 A ASN 335 HELX_P A TYR 484 A TYR 345 1 7 11 disulf 2.058 A CYS 54 A SG CYS 11 1_555 A CYS 74 A SG CYS 31 1_555 disulf 2.031 A CYS 119 A SG CYS 76 1_555 A CYS 205 A SG CYS 89 1_555 disulf 2.045 A CYS 218 A SG CYS 102 1_555 A CYS 247 A SG CYS 131 1_555 disulf 2.079 A CYS 228 A SG CYS 112 1_555 A CYS 239 A SG CYS 123 1_555 disulf 2.047 A CYS 296 A SG CYS 180 1_555 A CYS 331 A SG CYS 199 1_555 disulf 2.029 A CYS 378 A SG CYS 245 1_555 A CYS 445 A SG CYS 306 1_555 disulf 2.036 A CYS 385 A SG CYS 252 1_555 A CYS 418 A SG CYS 279 1_555 disulf 2.034 A CYS 395 A SG CYS 262 1_555 A CYS 410 A SG CYS 271 1_555 covale 1.309 one N-Glycosylation A ASN 234 A ND2 ASN 118 1_555 A NAG 734 B C1 NAG 1_555 covale 1.446 one N-Glycosylation A ASN 241 A ND2 ASN 125 1_555 A NAG 741 C C1 NAG 1_555 covale 1.448 one N-Glycosylation A ASN 262 A ND2 ASN 146 1_555 A NAG 762 D C1 NAG 1_555 covale 1.491 one N-Glycosylation A ASN 276 A ND2 ASN 160 1_555 A NAG 776 E C1 NAG 1_555 covale 1.445 one N-Glycosylation A ASN 289 A ND2 ASN 173 1_555 A NAG 789 F C1 NAG 1_555 covale 1.449 one N-Glycosylation A ASN 295 A ND2 ASN 179 1_555 A NAG 795 G C1 NAG 1_555 covale 1.434 one N-Glycosylation A ASN 334 A ND2 ASN 202 1_555 A NAG 834 H C1 NAG 1_555 covale 1.436 one N-Glycosylation A ASN 386 A ND2 ASN 253 1_555 A NAG 886 I C1 NAG 1_555 covale 1.451 one N-Glycosylation A ASN 392 A ND2 ASN 259 1_555 A NAG 892 J C1 NAG 1_555 covale 1.437 one N-Glycosylation A ASN 448 A ND2 ASN 309 1_555 A NAG 948 K C1 NAG 1_555 VIRAL PROTEIN HIV-1 gp120, unliganded structure, clade A/E 93TH057, VIRAL PROTEIN 3TGT PDB 1 3TGT 44 492 3TGT 44 492 3TGT A 1 1 353 5 3 2 4 5 7 anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A TRP 45 A TRP 2 A ASP 47 A ASP 4 A TYR 486 A TYR 347 A ILE 491 A ILE 352 A TYR 223 A TYR 107 A CYS 228 A CYS 112 A VAL 242 A VAL 126 A VAL 245 A VAL 129 A GLU 83 A GLU 40 A HIS 85 A HIS 42 A VAL 75 A VAL 32 A PRO 76 A PRO 33 A PHE 53 A PHE 10 A SER 56 A SER 13 A HIS 216 A HIS 100 A CYS 218 A CYS 102 A GLU 91 A GLU 48 A ASN 94 A ASN 51 A THR 236 A THR 120 A CYS 239 A CYS 123 A SER 199 A SER 83 A LYS 202 A LYS 86 A VAL 120 A VAL 77 A THR 123 A THR 80 A GLN 432 A GLN 293 A MET 434 A MET 295 A ILE 423 A ILE 284 A ASN 425 A ASN 286 A LEU 259 A LEU 143 A LEU 261 A LEU 145 A ILE 443 A ILE 304 A ARG 456 A ARG 317 A ILE 284 A ILE 168 A ARG 298 A ARG 182 A ASN 465 A ASN 326 A PRO 470 A PRO 331 A THR 358 A THR 225 A PHE 361 A PHE 228 A ILE 271 A ILE 155 A ARG 273 A ARG 157 A ILE 284 A ILE 168 A ARG 298 A ARG 182 A ILE 443 A ILE 304 A ARG 456 A ARG 317 A LYS 328 A LYS 196 A ASN 334 A ASN 202 A THR 413 A THR 274 A ILE 420 A ILE 281 A GLU 381 A GLU 248 A CYS 385 A CYS 252 A HIS 374 A HIS 241 A CYS 378 A CYS 245 19 P 21 21 21