0.022071 0.012743 0.000000 0.000000 0.025486 0.000000 0.000000 0.000000 0.023719 0.00000 0.00000 0.00000 Liu, J. Lu, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 45.308 45.308 42.160 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID 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 C30 H63 N O10 597.822 O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) JEFFAMINE non-polymer C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE 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 N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N O N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N N N 58 S C N 59 N C N 60 N O N 61 N C N 62 N C N 63 N C N 64 N O N 65 N N N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N N N 78 S C N 79 N C N 80 N O N 81 N C N 82 N C N 83 N C N 84 N O N 85 N O N 86 N O N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N N N 97 N C N 98 N C N 99 N O N 100 N O N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N N N 107 S C N 108 N C N 109 N O N 110 N C Y 111 N C Y 112 N N Y 113 N C Y 114 N C Y 115 N N N 116 N O N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N O N 128 N H N 129 N H N 130 N N N 131 S C N 132 N C N 133 N O N 134 S C N 135 N C N 136 N C N 137 N C N 138 N O N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N C N 153 N O N 154 N C N 155 N C N 156 N O N 157 N C N 158 N C N 159 N C N 160 N O N 161 N C N 162 N C N 163 N C N 164 N O N 165 R C N 166 N C N 167 N C N 168 N O N 169 R C N 170 N C N 171 N C N 172 N O N 173 S C N 174 N C N 175 N C N 176 N O N 177 S C N 178 N C N 179 N C N 180 N O N 181 R C N 182 N C N 183 N C N 184 N O N 185 R C N 186 N C N 187 N C N 188 N O N 189 N C N 190 N C N 191 N C N 192 N N N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N N N 257 S C N 258 N C N 259 N O N 260 N C N 261 N C N 262 N C N 263 N C N 264 N O N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N N N 279 S C N 280 N C N 281 N O N 282 N C N 283 N C N 284 N C N 285 N C N 286 N N N 287 N O N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N H N 296 N H N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N N N 304 S C N 305 N C N 306 N O N 307 R C N 308 N O N 309 N C N 310 N O N 311 N H N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N H N 319 N H N 320 N N N 321 S C N 322 N C N 323 N O N 324 N C Y 325 N C Y 326 N C Y 327 N C Y 328 N N Y 329 N C Y 330 N C Y 331 N C Y 332 N C Y 333 N C N 334 N O N 335 N H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N N N 348 S C N 349 N C N 350 N O N 351 N C Y 352 N C Y 353 N C Y 354 N C Y 355 N C Y 356 N C Y 357 N C N 358 N O N 359 N O N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H N 366 N H N 367 N H N 368 N H N 369 N H N 370 N H N 371 N N N 372 S C N 373 N C N 374 N O N 375 N C N 376 N C N 377 N C N 378 N O N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N doub N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N doub N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N doub N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N doub N 107 N sing N 108 N sing N 109 N sing N 110 N sing Y 111 N sing Y 112 N doub Y 113 N doub N 114 N sing Y 115 N sing N 116 N sing Y 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N doub N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N doub N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N doub N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N doub N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N doub N 315 N sing N 316 N sing N 317 N sing N 318 N sing Y 319 N doub Y 320 N sing Y 321 N sing N 322 N sing Y 323 N doub Y 324 N sing Y 325 N sing N 326 N sing Y 327 N sing Y 328 N doub N 329 N sing Y 330 N doub N 331 N sing Y 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N doub N 343 N sing N 344 N sing N 345 N sing N 346 N sing Y 347 N doub Y 348 N sing Y 349 N sing N 350 N sing Y 351 N doub N 352 N sing Y 353 N doub N 354 N sing Y 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N doub N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing To be Published 0353 Structural Determinants of Trimerization Specificity in HIV-1 gp41 Protein 10.2210/pdb3u91/pdb pdb_00003u91 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 CCD 2005-06-25 ADSC QUANTUM 4 SINGLE WAVELENGTH M x-ray 1 0.9676 1.0 X4A NSLS 0.9676 SYNCHROTRON NSLS BEAMLINE X4A 3936.581 Gp41 N-TERMINAL DOMAIN 1 man polymer 597.822 O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) 1 syn non-polymer 18.015 water 48 nat water no no EAQQHLLQLTVWGIKQLQARILAVERYLKDQQL EAQQHLLQLTVWGIKQLQARILAVERYLKDQQL 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 sample env 11676 Human immunodeficiency virus 1 562 Escherichia coli 1 3.17 61.24 VAPOR DIFFUSION, HANGING DROP 6.0 20% Jeffamine M600, 0.1M MES, 25mM Cesium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K 298 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_site repository Initial release Data collection Database references Derived calculations Refinement description 1 0 2013-04-24 1 1 2023-09-13 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2011-10-17 REL REL JEF O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) HOH water 1AIK PDB ENTRY 1AIK PDB experimental model JEF 1 2 JEF JEF 34 A WAT 35 3 HOH HOH 35 A WAT 36 3 HOH HOH 36 A WAT 37 3 HOH HOH 37 A WAT 38 3 HOH HOH 38 A WAT 39 3 HOH HOH 39 A WAT 40 3 HOH HOH 40 A WAT 41 3 HOH HOH 41 A WAT 42 3 HOH HOH 42 A WAT 43 3 HOH HOH 43 A WAT 44 3 HOH HOH 44 A WAT 45 3 HOH HOH 45 A WAT 46 3 HOH HOH 46 A WAT 47 3 HOH HOH 47 A WAT 48 3 HOH HOH 48 A WAT 49 3 HOH HOH 49 A WAT 2 3 HOH HOH 50 A WAT 3 3 HOH HOH 51 A WAT 4 3 HOH HOH 52 A WAT 5 3 HOH HOH 53 A WAT 6 3 HOH HOH 54 A WAT 7 3 HOH HOH 55 A WAT 8 3 HOH HOH 56 A WAT 9 3 HOH HOH 57 A WAT 10 3 HOH HOH 58 A WAT 11 3 HOH HOH 59 A WAT 12 3 HOH HOH 60 A WAT 13 3 HOH HOH 61 A WAT 14 3 HOH HOH 62 A WAT 15 3 HOH HOH 63 A WAT 16 3 HOH HOH 64 A WAT 17 3 HOH HOH 65 A WAT 18 3 HOH HOH 66 A WAT 19 3 HOH HOH 67 A WAT 20 3 HOH HOH 68 A WAT 21 3 HOH HOH 69 A WAT 22 3 HOH HOH 70 A WAT 23 3 HOH HOH 71 A WAT 24 3 HOH HOH 72 A WAT 25 3 HOH HOH 73 A WAT 26 3 HOH HOH 74 A WAT 27 3 HOH HOH 75 A WAT 28 3 HOH HOH 76 A WAT 29 3 HOH HOH 77 A WAT 30 3 HOH HOH 78 A WAT 31 3 HOH HOH 79 A WAT 32 3 HOH HOH 80 A WAT 33 3 HOH HOH 81 A WAT 34 3 HOH HOH 82 A n 1 1 A n 2 2 A n 3 3 A GLN 4 n 4 GLN 4 A HIS 5 n 5 HIS 5 A LEU 6 n 6 LEU 6 A LEU 7 n 7 LEU 7 A GLN 8 n 8 GLN 8 A LEU 9 n 9 LEU 9 A THR 10 n 10 THR 10 A VAL 11 n 11 VAL 11 A TRP 12 n 12 TRP 12 A GLY 13 n 13 GLY 13 A ILE 14 n 14 ILE 14 A LYS 15 n 15 LYS 15 A GLN 16 n 16 GLN 16 A LEU 17 n 17 LEU 17 A GLN 18 n 18 GLN 18 A ALA 19 n 19 ALA 19 A ARG 20 n 20 ARG 20 A ILE 21 n 21 ILE 21 A LEU 22 n 22 LEU 22 A ALA 23 n 23 ALA 23 A VAL 24 n 24 VAL 24 A GLU 25 n 25 GLU 25 A ARG 26 n 26 ARG 26 A TYR 27 n 27 TYR 27 A LEU 28 n 28 LEU 28 A LYS 29 n 29 LYS 29 A ASP 30 n 30 ASP 30 A GLN 31 n 31 GLN 31 A GLN 32 n 32 GLN 32 A LEU 33 n 33 LEU 33 A 1.0872 0.2375 -0.5490 1.3105 -0.8340 6.0814 -0.0522 0.1599 0.0426 -0.2306 0.0059 -0.0361 0.3026 0.1494 0.0463 -0.0559 0.0044 0.0076 -0.1179 0.0043 -0.1738 refined -21.5020 6.9580 -8.6230 X-RAY DIFFRACTION A 4 A 33 X-RAY DIFFRACTION 1 author_and_software_defined_assembly PISA 3 trimeric 4690 -31 6750 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 -0.5000000000 -0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_565 -y,x-y+1,z crystal symmetry operation -22.6540000000 39.2378789947 0.0000000000 -0.5000000000 0.8660254038 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_455 -x+y-1,-x,z crystal symmetry operation -45.3080000000 0.0000000000 0.0000000000 1 A HOH 67 C HOH 1 A C38 JEF 34 B C38 JEF 1 1 N 1 A O12 JEF 34 B O12 JEF 1 1 N 1 A C37 JEF 34 B C37 JEF 1 1 N 1 A C36 JEF 34 B C36 JEF 1 1 N 1 A O11 JEF 34 B O11 JEF 1 1 N 1 A C33 JEF 34 B C33 JEF 1 1 N 1 A C34 JEF 34 B C34 JEF 1 1 N 1 A C32 JEF 34 B C32 JEF 1 1 N 1 A O10 JEF 34 B O10 JEF 1 1 N 1 A C19 JEF 34 B C19 JEF 1 1 N 1 A C40 JEF 34 B C40 JEF 1 1 N 1 A O3 JEF 34 B O3 JEF 1 1 N 1 A C7 JEF 34 B C7 JEF 1 1 N 1 A C9 JEF 34 B C9 JEF 1 1 N 1 A C8 JEF 34 B C8 JEF 1 1 N 1 A O4 JEF 34 B O4 JEF 1 1 N 1 A C11 JEF 34 B C11 JEF 1 1 N 1 A C12 JEF 34 B C12 JEF 1 1 N 1 A C10 JEF 34 B C10 JEF 1 1 N 1 A O5 JEF 34 B O5 JEF 1 1 N 1 A C13 JEF 34 B C13 JEF 1 1 N 1 A C15 JEF 34 B C15 JEF 1 1 N 1 A C14 JEF 34 B C14 JEF 1 1 N 1 A O6 JEF 34 B O6 JEF 1 1 N 1 A C16 JEF 34 B C16 JEF 1 1 N 1 A C30 JEF 34 B C30 JEF 1 1 N 1 A C31 JEF 34 B C31 JEF 1 1 N 1 A N1 JEF 34 B N1 JEF 1 1 N 1 A GLU 1 A GLU 1 1 Y 1 A ALA 2 A ALA 2 1 Y 1 A GLN 3 A GLN 3 1 Y 26.142 0.62 0.31 0.00 0.62 0.00 -0.93 0.956 0.928 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.23341 0.19191 0.19585 1.45 42.14 917 9173 8256 10.0 99.85 1.818 0.037 RANDOM 1 Isotropic THROUGHOUT MOLECULAR REPLACEMENT 0.061 0.069 0.80 0.80 1.20 PDB ENTRY 1AIK MAXIMUM LIKELIHOOD BABINET MODEL WITH MASK 1.45 42.14 48 316 13 0 255 0.009 0.022 270 1.138 2.010 362 4.226 5.000 29 37.213 24.615 13 12.035 15.000 53 7.733 15.000 2 0.073 0.200 44 0.005 0.020 186 0.206 0.200 115 0.301 0.200 185 0.130 0.200 20 0.138 0.200 47 0.103 0.200 11 0.784 1.500 152 1.420 2.000 239 2.362 3.000 131 3.846 4.500 123 0.250 0.202 1.489 72 568 20 99.69 1.45 42.14 3U91 9173 0.065 1 9.1 8.8 99.8 1.45 1.50 6.4 0.467 1 8.8 99.8 data collection ADSC Quantum phasing PHASER refinement REFMAC 5.2.0005 data reduction HKL-2000 data scaling HKL-2000 Structural Determinants of Trimerization Specificity in HIV-1 gp41 Protein 1 N N 2 N N 3 N N A HIS 5 A HIS 5 HELX_P A GLN 31 A GLN 31 1 1 27 VIRAL PROTEIN gp41, HIV-1, trimerization domain, oligomeric structure, VIRAL PROTEIN Q9YYZ1_9HIV1 UNP 1 7 Q9YYZ1 EAQQHLLQLTVWGIKQLQARILAVERYLKDQQL 7 39 3U91 1 33 Q9YYZ1 A 1 1 33 BINDING SITE FOR RESIDUE JEF A 34 A JEF 34 Software 6 A GLU 25 A GLU 25 6 2_565 A TYR 27 A TYR 27 6 1_555 A LEU 28 A LEU 28 6 2_565 A LYS 29 A LYS 29 6 2_565 A LEU 33 A LEU 33 6 2_565 A HOH 41 C HOH 6 1_555 150 P 3 2 1