0.027173 -0.001681 -0.004858 0.000000 0.024857 -0.010486 0.000000 0.000000 0.024880 0.00000 0.00000 0.00000 Naur, P. Vestergaard, B. Gajhede, M. Kastrup, J.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 66.88 79.31 86.46 36.801 40.307 44.393 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 Cl -1 35.453 CHLORIDE ION non-polymer C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C3 H7 N O3 105.093 D-SERINE D-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 Na 1 22.990 SODIUM ION non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C N S -1 58.082 THIOCYANATE ION non-polymer 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 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 N 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 H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O 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 CL N 75 N N N 76 R C N 77 N C N 78 N O N 79 N C N 80 N S N 81 N O N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N N N 90 R C N 91 N C N 92 N O N 93 N O N 94 N C N 95 N O N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N N N 104 S C N 105 N C N 106 N O N 107 N C N 108 N C N 109 N C N 110 N O N 111 N N N 112 N O N 113 N H N 114 N H N 115 N H N 116 N H 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 N N 124 S C N 125 N C N 126 N O N 127 N C N 128 N C N 129 N C N 130 N O N 131 N O N 132 N O N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N N N 143 N C N 144 N C N 145 N O N 146 N O N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N N N 153 S C N 154 N C N 155 N O N 156 N C Y 157 N C Y 158 N N Y 159 N C Y 160 N C Y 161 N N N 162 N O N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N O N 174 N H N 175 N H N 176 N N N 177 S C N 178 N C N 179 N O N 180 S C N 181 N C N 182 N C N 183 N C N 184 N O N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N N N 199 S C N 200 N C N 201 N O N 202 N C N 203 N C N 204 N C N 205 N C N 206 N O 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 N N 221 S C N 222 N C N 223 N O N 224 N C N 225 N C N 226 N C N 227 N C N 228 N N N 229 N O 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 N N 246 S C N 247 N C N 248 N O N 249 N C N 250 N C N 251 N S N 252 N C N 253 N O N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N NA N 266 N N N 267 S C N 268 N C N 269 N O N 270 N C Y 271 N C Y 272 N C Y 273 N C Y 274 N C Y 275 N C Y 276 N C N 277 N O N 278 N H N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N N N 290 S C N 291 N C N 292 N O N 293 N C N 294 N C N 295 N C N 296 N O 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 H N 304 N H N 305 N H N 306 N S N 307 N C N 308 N N N 309 N N N 310 S C N 311 N C N 312 N O N 313 N C N 314 N O N 315 N O N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N H N 322 N H N 323 N N N 324 S C N 325 N C N 326 N O N 327 R C N 328 N O N 329 N C N 330 N O N 331 N H N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N N N 341 S C N 342 N C N 343 N O N 344 N C Y 345 N C Y 346 N C Y 347 N C Y 348 N N Y 349 N C Y 350 N C Y 351 N C Y 352 N C Y 353 N C N 354 N O N 355 N H N 356 N H N 357 N H N 358 N H N 359 N H 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 N N 368 S C N 369 N C N 370 N O N 371 N C Y 372 N C Y 373 N C Y 374 N C Y 375 N C Y 376 N C Y 377 N C N 378 N O N 379 N O 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 390 N H N 391 N N N 392 S C N 393 N C N 394 N O N 395 N C N 396 N C N 397 N C N 398 N O N 399 N H N 400 N H N 401 N H N 402 N H N 403 N H N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 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 sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N sing 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 doub N 77 N sing N 78 N sing N 79 N sing 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 sing N 88 N sing N 89 N doub 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 sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N doub N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N doub N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N doub 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 doub 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 doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing Y 153 N sing Y 154 N doub Y 155 N doub N 156 N sing Y 157 N sing N 158 N sing Y 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 doub 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 doub 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 doub 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 doub 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 sing N 254 N sing N 255 N sing N 256 N doub N 257 N sing N 258 N sing N 259 N sing N 260 N sing Y 261 N doub Y 262 N sing Y 263 N sing N 264 N sing Y 265 N doub N 266 N sing Y 267 N doub N 268 N sing Y 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N doub 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 trip 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 doub N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N doub N 328 N sing N 329 N sing N 330 N sing N 331 N sing Y 332 N doub Y 333 N sing Y 334 N sing N 335 N sing Y 336 N doub Y 337 N sing Y 338 N sing N 339 N sing Y 340 N sing Y 341 N doub N 342 N sing Y 343 N doub N 344 N sing Y 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N doub N 356 N sing N 357 N sing N 358 N sing N 359 N sing Y 360 N doub Y 361 N sing Y 362 N sing N 363 N sing Y 364 N doub N 365 N sing Y 366 N doub N 367 N sing Y 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 N 378 N sing N 379 N doub N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 104 14116 10.1073/PNAS.0703718104 17715062 Ionotropic Glutamate-Like Receptor {Delta}2 Binds D-Serine and Glycine. 2007 10.2210/pdb2v3u/pdb pdb_00002v3u 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 2006-01-14 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.95373 1.0 14.1 BESSY 0.95373 SYNCHROTRON BESSY BEAMLINE 14.1 29937.670 GLUTAMATE RECEPTOR DELTA-2 SUBUNIT LIGAND-BINDING CORE, RESIDUES 440-551,664-813 1 man polymer 105.093 D-SERINE 1 syn non-polymer 22.990 SODIUM ION 1 syn non-polymer 35.453 CHLORIDE ION 1 syn non-polymer 58.082 THIOCYANATE ION 2 syn non-polymer 18.015 water 135 nat water GLURDELTA2, GLUR DELTA-2 no no GGVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRAD IGISALTITPDRENVVDFTTRYMDYSVGVLLRRGTSIQSLQDLSKQTDIPYGTVLDSAVYQHVRMKGLNPFERDSMYSQM WRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRI LELQQSGDMDILKHKWWPKNGQCDL GGVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRAD IGISALTITPDRENVVDFTTRYMDYSVGVLLRRGTSIQSLQDLSKQTDIPYGTVLDSAVYQHVRMKGLNPFERDSMYSQM WRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRI LELQQSGDMDILKHKWWPKNGQCDL 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 RAT sample 10116 RATTUS NORVEGICUS 562 ESCHERICHIA COLI ORIGAMI 2 PET28 1 2 40 THE TWO SEPARATE DOMAINS OF THE APO STRUCTURE WERE USED AS SEARCH MODELS AS BINDING OF D-SERINE WAS EXPECTED TO INDUCE CONFORMATIONAL CHANGES. VAPOR DIFFUSION, HANGING DROP 6.5 HANGING DROP VAPOR DIFFUSION. 20% PEG4000, 0.1 M CACODYLATE PH 6.5, 0.2 M SODIUM THIOCYANATE database_PDB_rev database_PDB_rev_record exptl_crystal_grow pdbx_database_proc pdbx_database_status chem_comp_atom chem_comp_bond database_2 pdbx_database_status pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn repository Initial release Version format compliance Version format compliance Data collection Experimental preparation Other Data collection Database references Derived calculations Other Refinement description 1 0 2007-08-07 1 1 2011-05-08 1 2 2011-07-13 1 3 2019-05-08 1 4 2023-12-13 _exptl_crystal_grow.method _pdbx_database_status.recvd_author_approval _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_sf _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id STRUCTURE OF THE LIGAND-BINDING CORE OF THE IONOTROPIC GLUTAMATE RECEPTOR-LIKE GLURDELTA2 IN THE APO FORM PDBE Y PDBE 2007-06-22 REL REL DSN D-SERINE NA SODIUM ION CL CHLORIDE ION SCN THIOCYANATE ION HOH water THE NATIVE GLURDELTA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS THE EXTRACELLULAR LIGAND-BINDING CORE OF GLURDELTA2. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER. CONSEQUENTLY, THE PROTEIN SEQUENCE MATCHES DISCONTINOUSLY WITH THE REFERENCE DATABASE. THE FIRST GLYCINE OF THE SEQUENCE IS A REMNANT OF A TRYPSIN CLEVAGE SITE 2V3T PDB ENTRY 2V3T PDB experimental model DSN 1262 2 DSN DSN 1262 A NA 1263 3 NA NA 1263 A CL 1264 4 CL CL 1264 A SCN 1265 5 SCN SCN 1265 A SCN 1266 5 SCN SCN 1266 A HOH 2001 6 HOH HOH 2001 A HOH 2002 6 HOH HOH 2002 A HOH 2003 6 HOH HOH 2003 A HOH 2004 6 HOH HOH 2004 A HOH 2005 6 HOH HOH 2005 A HOH 2006 6 HOH HOH 2006 A HOH 2007 6 HOH HOH 2007 A HOH 2008 6 HOH HOH 2008 A HOH 2009 6 HOH HOH 2009 A HOH 2010 6 HOH HOH 2010 A HOH 2011 6 HOH HOH 2011 A HOH 2012 6 HOH HOH 2012 A HOH 2013 6 HOH HOH 2013 A HOH 2014 6 HOH HOH 2014 A HOH 2015 6 HOH HOH 2015 A HOH 2016 6 HOH HOH 2016 A HOH 2017 6 HOH HOH 2017 A HOH 2018 6 HOH HOH 2018 A HOH 2019 6 HOH HOH 2019 A HOH 2020 6 HOH HOH 2020 A HOH 2021 6 HOH HOH 2021 A HOH 2022 6 HOH HOH 2022 A HOH 2023 6 HOH HOH 2023 A HOH 2024 6 HOH HOH 2024 A HOH 2025 6 HOH HOH 2025 A HOH 2026 6 HOH HOH 2026 A HOH 2027 6 HOH HOH 2027 A HOH 2028 6 HOH HOH 2028 A HOH 2029 6 HOH HOH 2029 A HOH 2030 6 HOH HOH 2030 A HOH 2031 6 HOH HOH 2031 A HOH 2032 6 HOH HOH 2032 A HOH 2033 6 HOH HOH 2033 A HOH 2034 6 HOH HOH 2034 A HOH 2035 6 HOH HOH 2035 A HOH 2036 6 HOH HOH 2036 A HOH 2037 6 HOH HOH 2037 A HOH 2038 6 HOH HOH 2038 A HOH 2039 6 HOH HOH 2039 A HOH 2040 6 HOH HOH 2040 A HOH 2041 6 HOH HOH 2041 A HOH 2042 6 HOH HOH 2042 A HOH 2043 6 HOH HOH 2043 A HOH 2044 6 HOH HOH 2044 A HOH 2045 6 HOH HOH 2045 A HOH 2046 6 HOH HOH 2046 A HOH 2047 6 HOH HOH 2047 A HOH 2048 6 HOH HOH 2048 A HOH 2049 6 HOH HOH 2049 A HOH 2050 6 HOH HOH 2050 A HOH 2051 6 HOH HOH 2051 A HOH 2052 6 HOH HOH 2052 A HOH 2053 6 HOH HOH 2053 A HOH 2054 6 HOH HOH 2054 A HOH 2055 6 HOH HOH 2055 A HOH 2056 6 HOH HOH 2056 A HOH 2057 6 HOH HOH 2057 A HOH 2058 6 HOH HOH 2058 A HOH 2059 6 HOH HOH 2059 A HOH 2060 6 HOH HOH 2060 A HOH 2061 6 HOH HOH 2061 A HOH 2062 6 HOH HOH 2062 A HOH 2063 6 HOH HOH 2063 A HOH 2064 6 HOH HOH 2064 A HOH 2065 6 HOH HOH 2065 A HOH 2066 6 HOH HOH 2066 A HOH 2067 6 HOH HOH 2067 A HOH 2068 6 HOH HOH 2068 A HOH 2069 6 HOH HOH 2069 A HOH 2070 6 HOH HOH 2070 A HOH 2071 6 HOH HOH 2071 A HOH 2072 6 HOH HOH 2072 A HOH 2073 6 HOH HOH 2073 A HOH 2074 6 HOH HOH 2074 A HOH 2075 6 HOH HOH 2075 A HOH 2076 6 HOH HOH 2076 A HOH 2077 6 HOH HOH 2077 A HOH 2078 6 HOH HOH 2078 A HOH 2079 6 HOH HOH 2079 A HOH 2080 6 HOH HOH 2080 A HOH 2081 6 HOH HOH 2081 A HOH 2082 6 HOH HOH 2082 A HOH 2083 6 HOH HOH 2083 A HOH 2084 6 HOH HOH 2084 A HOH 2085 6 HOH HOH 2085 A HOH 2086 6 HOH HOH 2086 A HOH 2087 6 HOH HOH 2087 A HOH 2088 6 HOH HOH 2088 A HOH 2089 6 HOH HOH 2089 A HOH 2090 6 HOH HOH 2090 A HOH 2091 6 HOH HOH 2091 A HOH 2092 6 HOH HOH 2092 A HOH 2093 6 HOH HOH 2093 A HOH 2094 6 HOH HOH 2094 A HOH 2095 6 HOH HOH 2095 A HOH 2096 6 HOH HOH 2096 A HOH 2097 6 HOH HOH 2097 A HOH 2098 6 HOH HOH 2098 A HOH 2099 6 HOH HOH 2099 A HOH 2100 6 HOH HOH 2100 A HOH 2101 6 HOH HOH 2101 A HOH 2102 6 HOH HOH 2102 A HOH 2103 6 HOH HOH 2103 A HOH 2104 6 HOH HOH 2104 A HOH 2105 6 HOH HOH 2105 A HOH 2106 6 HOH HOH 2106 A HOH 2107 6 HOH HOH 2107 A HOH 2108 6 HOH HOH 2108 A HOH 2109 6 HOH HOH 2109 A HOH 2110 6 HOH HOH 2110 A HOH 2111 6 HOH HOH 2111 A HOH 2112 6 HOH HOH 2112 A HOH 2113 6 HOH HOH 2113 A HOH 2114 6 HOH HOH 2114 A HOH 2115 6 HOH HOH 2115 A HOH 2116 6 HOH HOH 2116 A HOH 2117 6 HOH HOH 2117 A HOH 2118 6 HOH HOH 2118 A HOH 2119 6 HOH HOH 2119 A HOH 2120 6 HOH HOH 2120 A HOH 2121 6 HOH HOH 2121 A HOH 2122 6 HOH HOH 2122 A HOH 2123 6 HOH HOH 2123 A HOH 2124 6 HOH HOH 2124 A HOH 2125 6 HOH HOH 2125 A HOH 2126 6 HOH HOH 2126 A HOH 2127 6 HOH HOH 2127 A HOH 2128 6 HOH HOH 2128 A HOH 2129 6 HOH HOH 2129 A HOH 2130 6 HOH HOH 2130 A HOH 2131 6 HOH HOH 2131 A HOH 2132 6 HOH HOH 2132 A HOH 2133 6 HOH HOH 2133 A HOH 2134 6 HOH HOH 2134 A HOH 2135 6 HOH HOH 2135 A GLY 1 n 1 GLY 1 A GLY 2 n 2 GLY 2 A VAL 3 n 3 VAL 3 A VAL 4 n 4 VAL 4 A LEU 5 n 5 LEU 5 A ARG 6 n 6 ARG 6 A VAL 7 n 7 VAL 7 A VAL 8 n 8 VAL 8 A THR 9 n 9 THR 9 A VAL 10 n 10 VAL 10 A LEU 11 n 11 LEU 11 A GLU 12 n 12 GLU 12 A GLU 13 n 13 GLU 13 A PRO 14 n 14 PRO 14 A PHE 15 n 15 PHE 15 A VAL 16 n 16 VAL 16 A MET 17 n 17 MET 17 A VAL 18 n 18 VAL 18 A SER 19 n 19 SER 19 A GLU 20 n 20 GLU 20 A ASN 21 n 21 ASN 21 A VAL 22 n 22 VAL 22 A LEU 23 n 23 LEU 23 A GLY 24 n 24 GLY 24 A LYS 25 n 25 LYS 25 A PRO 26 n 26 PRO 26 A LYS 27 n 27 LYS 27 A LYS 28 n 28 LYS 28 A TYR 29 n 29 TYR 29 A GLN 30 n 30 GLN 30 A GLY 31 n 31 GLY 31 A PHE 32 n 32 PHE 32 A SER 33 n 33 SER 33 A ILE 34 n 34 ILE 34 A ASP 35 n 35 ASP 35 A VAL 36 n 36 VAL 36 A LEU 37 n 37 LEU 37 A ASP 38 n 38 ASP 38 A ALA 39 n 39 ALA 39 A LEU 40 n 40 LEU 40 A SER 41 n 41 SER 41 A ASN 42 n 42 ASN 42 A TYR 43 n 43 TYR 43 A LEU 44 n 44 LEU 44 A GLY 45 n 45 GLY 45 A PHE 46 n 46 PHE 46 A ASN 47 n 47 ASN 47 A TYR 48 n 48 TYR 48 A GLU 49 n 49 GLU 49 A ILE 50 n 50 ILE 50 A TYR 51 n 51 TYR 51 A VAL 52 n 52 VAL 52 A ALA 53 n 53 ALA 53 A PRO 54 n 54 PRO 54 A ASP 55 n 55 ASP 55 A HIS 56 n 56 HIS 56 A LYS 57 n 57 LYS 57 A TYR 58 n 58 TYR 58 A GLY 59 n 59 GLY 59 A SER 60 n 60 SER 60 A PRO 61 n 61 PRO 61 A GLN 62 n 62 GLN 62 A GLU 63 n 63 GLU 63 A ASP 64 n 64 ASP 64 A GLY 65 n 65 GLY 65 A THR 66 n 66 THR 66 A TRP 67 n 67 TRP 67 A ASN 68 n 68 ASN 68 A GLY 69 n 69 GLY 69 A LEU 70 n 70 LEU 70 A VAL 71 n 71 VAL 71 A GLY 72 n 72 GLY 72 A GLU 73 n 73 GLU 73 A LEU 74 n 74 LEU 74 A VAL 75 n 75 VAL 75 A PHE 76 n 76 PHE 76 A LYS 77 n 77 LYS 77 A ARG 78 n 78 ARG 78 A ALA 79 n 79 ALA 79 A ASP 80 n 80 ASP 80 A ILE 81 n 81 ILE 81 A GLY 82 n 82 GLY 82 A ILE 83 n 83 ILE 83 A SER 84 n 84 SER 84 A ALA 85 n 85 ALA 85 A LEU 86 n 86 LEU 86 A THR 87 n 87 THR 87 A ILE 88 n 88 ILE 88 A THR 89 n 89 THR 89 A PRO 90 n 90 PRO 90 A ASP 91 n 91 ASP 91 A ARG 92 n 92 ARG 92 A GLU 93 n 93 GLU 93 A ASN 94 n 94 ASN 94 A VAL 95 n 95 VAL 95 A VAL 96 n 96 VAL 96 A ASP 97 n 97 ASP 97 A PHE 98 n 98 PHE 98 A THR 99 n 99 THR 99 A THR 100 n 100 THR 100 A ARG 101 n 101 ARG 101 A TYR 102 n 102 TYR 102 A MET 103 n 103 MET 103 A ASP 104 n 104 ASP 104 A TYR 105 n 105 TYR 105 A SER 106 n 106 SER 106 A VAL 107 n 107 VAL 107 A GLY 108 n 108 GLY 108 A VAL 109 n 109 VAL 109 A LEU 110 n 110 LEU 110 A LEU 111 n 111 LEU 111 A ARG 112 n 112 ARG 112 A ARG 113 n 113 ARG 113 A GLY 114 n 114 GLY 114 A THR 115 n 115 THR 115 A SER 116 n 116 SER 116 A ILE 117 n 117 ILE 117 A GLN 118 n 118 GLN 118 A SER 119 n 119 SER 119 A LEU 120 n 120 LEU 120 A GLN 121 n 121 GLN 121 A ASP 122 n 122 ASP 122 A LEU 123 n 123 LEU 123 A SER 124 n 124 SER 124 A LYS 125 n 125 LYS 125 A GLN 126 n 126 GLN 126 A THR 127 n 127 THR 127 A ASP 128 n 128 ASP 128 A ILE 129 n 129 ILE 129 A PRO 130 n 130 PRO 130 A TYR 131 n 131 TYR 131 A GLY 132 n 132 GLY 132 A THR 133 n 133 THR 133 A VAL 134 n 134 VAL 134 A LEU 135 n 135 LEU 135 A ASP 136 n 136 ASP 136 A SER 137 n 137 SER 137 A ALA 138 n 138 ALA 138 A VAL 139 n 139 VAL 139 A TYR 140 n 140 TYR 140 A GLN 141 n 141 GLN 141 A HIS 142 n 142 HIS 142 A VAL 143 n 143 VAL 143 A ARG 144 n 144 ARG 144 A MET 145 n 145 MET 145 A LYS 146 n 146 LYS 146 A GLY 147 n 147 GLY 147 A LEU 148 n 148 LEU 148 A ASN 149 n 149 ASN 149 A PRO 150 n 150 PRO 150 A PHE 151 n 151 PHE 151 A GLU 152 n 152 GLU 152 A ARG 153 n 153 ARG 153 A ASP 154 n 154 ASP 154 A SER 155 n 155 SER 155 A MET 156 n 156 MET 156 A TYR 157 n 157 TYR 157 A SER 158 n 158 SER 158 A GLN 159 n 159 GLN 159 A MET 160 n 160 MET 160 A TRP 161 n 161 TRP 161 A ARG 162 n 162 ARG 162 A MET 163 n 163 MET 163 A ILE 164 n 164 ILE 164 A ASN 165 n 165 ASN 165 A ARG 166 n 166 ARG 166 A n 167 167 A n 168 168 A n 169 169 A n 170 170 A n 171 171 A ASN 172 n 172 ASN 172 A ASN 173 n 173 ASN 173 A VAL 174 n 174 VAL 174 A LEU 175 n 175 LEU 175 A GLU 176 n 176 GLU 176 A SER 177 n 177 SER 177 A GLN 178 n 178 GLN 178 A ALA 179 n 179 ALA 179 A GLY 180 n 180 GLY 180 A ILE 181 n 181 ILE 181 A GLN 182 n 182 GLN 182 A LYS 183 n 183 LYS 183 A VAL 184 n 184 VAL 184 A LYS 185 n 185 LYS 185 A TYR 186 n 186 TYR 186 A GLY 187 n 187 GLY 187 A ASN 188 n 188 ASN 188 A TYR 189 n 189 TYR 189 A ALA 190 n 190 ALA 190 A PHE 191 n 191 PHE 191 A VAL 192 n 192 VAL 192 A TRP 193 n 193 TRP 193 A ASP 194 n 194 ASP 194 A ALA 195 n 195 ALA 195 A ALA 196 n 196 ALA 196 A VAL 197 n 197 VAL 197 A LEU 198 n 198 LEU 198 A GLU 199 n 199 GLU 199 A TYR 200 n 200 TYR 200 A VAL 201 n 201 VAL 201 A ALA 202 n 202 ALA 202 A ILE 203 n 203 ILE 203 A ASN 204 n 204 ASN 204 A ASP 205 n 205 ASP 205 A PRO 206 n 206 PRO 206 A ASP 207 n 207 ASP 207 A CYS 208 n 208 CYS 208 A SER 209 n 209 SER 209 A PHE 210 n 210 PHE 210 A TYR 211 n 211 TYR 211 A THR 212 n 212 THR 212 A VAL 213 n 213 VAL 213 A GLY 214 n 214 GLY 214 A n 215 215 A n 216 216 A n 217 217 A ALA 218 n 218 ALA 218 A ASP 219 n 219 ASP 219 A ARG 220 n 220 ARG 220 A GLY 221 n 221 GLY 221 A TYR 222 n 222 TYR 222 A GLY 223 n 223 GLY 223 A ILE 224 n 224 ILE 224 A ALA 225 n 225 ALA 225 A LEU 226 n 226 LEU 226 A GLN 227 n 227 GLN 227 A HIS 228 n 228 HIS 228 A GLY 229 n 229 GLY 229 A SER 230 n 230 SER 230 A PRO 231 n 231 PRO 231 A TYR 232 n 232 TYR 232 A ARG 233 n 233 ARG 233 A ASP 234 n 234 ASP 234 A VAL 235 n 235 VAL 235 A PHE 236 n 236 PHE 236 A SER 237 n 237 SER 237 A GLN 238 n 238 GLN 238 A ARG 239 n 239 ARG 239 A ILE 240 n 240 ILE 240 A LEU 241 n 241 LEU 241 A GLU 242 n 242 GLU 242 A LEU 243 n 243 LEU 243 A GLN 244 n 244 GLN 244 A GLN 245 n 245 GLN 245 A SER 246 n 246 SER 246 A GLY 247 n 247 GLY 247 A ASP 248 n 248 ASP 248 A MET 249 n 249 MET 249 A ASP 250 n 250 ASP 250 A ILE 251 n 251 ILE 251 A LEU 252 n 252 LEU 252 A LYS 253 n 253 LYS 253 A HIS 254 n 254 HIS 254 A LYS 255 n 255 LYS 255 A TRP 256 n 256 TRP 256 A TRP 257 n 257 TRP 257 A PRO 258 n 258 PRO 258 A LYS 259 n 259 LYS 259 A ASN 260 n 260 ASN 260 A GLY 261 n 261 GLY 261 A n 262 262 A n 263 263 A n 264 264 A n 265 265 A author_and_software_defined_assembly PQS 1 monomeric A GLU 93 A O GLU 93 1_555 A NA 1263 C NA NA 1_555 A GLU 93 A OE2 GLU 93 1_555 91.9 A GLU 93 A O GLU 93 1_555 A NA 1263 C NA NA 1_555 A VAL 96 A O VAL 96 1_555 79.9 A GLU 93 A OE2 GLU 93 1_555 A NA 1263 C NA NA 1_555 A VAL 96 A O VAL 96 1_555 89.0 A GLU 93 A O GLU 93 1_555 A NA 1263 C NA NA 1_555 A ASP 97 A OD1 ASP 97 1_555 163.5 A GLU 93 A OE2 GLU 93 1_555 A NA 1263 C NA NA 1_555 A ASP 97 A OD1 ASP 97 1_555 92.6 A VAL 96 A O VAL 96 1_555 A NA 1263 C NA NA 1_555 A ASP 97 A OD1 ASP 97 1_555 84.4 A GLU 93 A O GLU 93 1_555 A NA 1263 C NA NA 1_555 A HOH 2054 G O HOH 1_555 94.2 A GLU 93 A OE2 GLU 93 1_555 A NA 1263 C NA NA 1_555 A HOH 2054 G O HOH 1_555 93.5 A VAL 96 A O VAL 96 1_555 A NA 1263 C NA NA 1_555 A HOH 2054 G O HOH 1_555 173.6 A ASP 97 A OD1 ASP 97 1_555 A NA 1263 C NA NA 1_555 A HOH 2054 G O HOH 1_555 101.3 A GLU 93 A O GLU 93 1_555 A NA 1263 C NA NA 1_555 A HOH 2114 G O HOH 1_555 84.6 A GLU 93 A OE2 GLU 93 1_555 A NA 1263 C NA NA 1_555 A HOH 2114 G O HOH 1_555 175.1 A VAL 96 A O VAL 96 1_555 A NA 1263 C NA NA 1_555 A HOH 2114 G O HOH 1_555 86.9 A ASP 97 A OD1 ASP 97 1_555 A NA 1263 C NA NA 1_555 A HOH 2114 G O HOH 1_555 89.8 A HOH 2054 G O HOH 1_555 A NA 1263 C NA NA 1_555 A HOH 2114 G O HOH 1_555 90.2 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 GLU 49 A N GLU 49 A O LEU 5 A O LEU 5 A N VAL 8 A N VAL 8 A O ILE 81 A O ILE 81 A N GLY 82 A N GLY 82 A O ALA 225 A O ALA 225 A N LEU 226 A N LEU 226 A O ASP 97 A O ASP 97 A N SER 19 A N SER 19 A O LYS 28 A O LYS 28 A N TYR 105 A N TYR 105 A O ARG 220 A O ARG 220 A N GLY 132 A N GLY 132 A O ALA 190 A O ALA 190 A N TRP 193 A N TRP 193 A O GLY 108 A O GLY 108 A N LEU 111 A N LEU 111 A O TYR 211 A O TYR 211 1 A SER 167 A SER 167 1 Y 1 A ASN 168 A ASN 168 1 Y 1 A GLY 169 A GLY 169 1 Y 1 A SER 170 A SER 170 1 Y 1 A GLU 171 A GLU 171 1 Y 1 A ASN 215 A ASN 215 1 Y 1 A THR 216 A THR 216 1 Y 1 A VAL 217 A VAL 217 1 Y 1 A GLN 262 A GLN 262 1 Y 1 A CYS 263 A CYS 263 1 Y 1 A ASP 264 A ASP 264 1 Y 1 A LEU 265 A LEU 265 1 Y 1 A A GLU GLU 12 13 -148.34 1 A A VAL SER 18 19 147.28 1 A GLU 12 -172.82 125.44 1 A PRO 14 -96.89 36.13 1 A SER 84 -161.87 -130.21 1 A ASN 165 -37.13 118.13 24.16 -0.73000 0.26000 0.54000 0.64000 -0.07000 -0.09000 0.954 0.923 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 167-171, 215-217 AND 262-265 ARE DISORDERED AND COULD NOT BE MODELED. 0.250 0.197 0.200 1.74 40.19 1154 21250 5.200 95.3 2.762 0.091 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.148 0.144 0.80 0.80 1.20 PDB ENTRY 2V3T MAXIMUM LIKELIHOOD MASK 1.74 40.19 135 2172 15 0 2022 0.016 0.022 2088 1.526 1.951 2827 11.478 5.000 250 38.776 24.175 103 15.315 15.000 347 17.371 15.000 13 0.111 0.200 306 0.007 0.020 1598 0.214 0.200 999 0.312 0.200 1431 0.136 0.200 151 0.221 0.200 46 0.127 0.200 12 1.019 1.500 1262 1.750 2.000 2035 2.415 3.000 867 3.785 4.500 792 0.3470 0.2700 1.79 80 1378 20 23.59 1.73 40.00 2V3U 23508 6.0 0.04 1 12.00 3.8 92.3 0.26 1.73 1.82 2.10 1 3.3 70.1 refinement REFMAC 5.2.0016 data reduction MOSFLM data scaling SCALA phasing PHASER Structure of the ligand-binding core of the ionotropic glutamate receptor-like GluRdelta2 in complex with D-serine 1 N N 2 N N 3 N N 4 N N 5 N N 5 N N 6 N N A GLY 31 A GLY 31 HELX_P A GLY 45 A GLY 45 1 1 15 A ASN 68 A ASN 68 HELX_P A PHE 76 A PHE 76 1 2 9 A THR 89 A THR 89 HELX_P A ASN 94 A ASN 94 1 3 6 A SER 119 A SER 119 HELX_P A LYS 125 A LYS 125 1 4 7 A SER 137 A SER 137 HELX_P A LEU 148 A LEU 148 1 5 12 A SER 155 A SER 155 HELX_P A ASN 165 A ASN 165 1 6 11 A GLU 176 A GLU 176 HELX_P A GLY 187 A GLY 187 1 7 12 A ALA 195 A ALA 195 HELX_P A ASP 205 A ASP 205 1 8 11 A TYR 232 A TYR 232 HELX_P A SER 246 A SER 246 1 9 15 A GLY 247 A GLY 247 HELX_P A TRP 257 A TRP 257 1 10 11 metalc 2.339 A GLU 93 A O GLU 93 1_555 A NA 1263 C NA NA 1_555 metalc 2.450 A GLU 93 A OE2 GLU 93 1_555 A NA 1263 C NA NA 1_555 metalc 2.572 A VAL 96 A O VAL 96 1_555 A NA 1263 C NA NA 1_555 metalc 2.305 A ASP 97 A OD1 ASP 97 1_555 A NA 1263 C NA NA 1_555 metalc 2.343 A NA 1263 C NA NA 1_555 A HOH 2054 G O HOH 1_555 metalc 2.473 A NA 1263 C NA NA 1_555 A HOH 2114 G O HOH 1_555 RECEPTOR POSTSYNAPTIC MEMBRANE, IONOTROPIC GLUTAMATE RECEPTORS, TRANSMEMBRANE, MEMBRANE PROTEIN, LIGAND-BINDING CORE, GLYCOPROTEIN, IONIC CHANNEL, ION TRANSPORT, MEMBRANE, RECEPTOR, D-SERINE, TRANSPORT A GLU 13 A GLU 13 1 A PRO 14 A PRO 14 -8.56 2V3U PDB 1 2V3U GRID2_RAT UNP 1 Q63226 1 1 2V3U 1 1 2V3U A 1 1 1 440 551 2V3U 2 113 Q63226 A 2 2 113 114 115 2V3U 114 115 2V3U A 1 114 115 664 813 2V3U 116 265 Q63226 A 2 116 265 5 2 2 4 parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel A ASN 47 A ASN 47 A VAL 52 A VAL 52 A VAL 4 A VAL 4 A THR 9 A THR 9 A ILE 81 A ILE 81 A GLY 82 A GLY 82 A ALA 225 A ALA 225 A GLN 227 A GLN 227 A VAL 96 A VAL 96 A PHE 98 A PHE 98 A MET 17 A MET 17 A SER 19 A SER 19 A LYS 28 A LYS 28 A GLN 30 A GLN 30 A MET 103 A MET 103 A TYR 105 A TYR 105 A ARG 220 A ARG 220 A TYR 222 A TYR 222 A TYR 131 A TYR 131 A GLY 132 A GLY 132 A ALA 190 A ALA 190 A ASP 194 A ASP 194 A VAL 107 A VAL 107 A ARG 112 A ARG 112 A PHE 210 A PHE 210 A VAL 213 A VAL 213 BINDING SITE FOR RESIDUE DSN A1262 Software 10 BINDING SITE FOR RESIDUE NA A1263 Software 5 BINDING SITE FOR RESIDUE CL A1264 Software 3 BINDING SITE FOR RESIDUE SCN A1265 Software 4 BINDING SITE FOR RESIDUE SCN A1266 Software 4 A TYR 58 A TYR 58 10 1_555 A ALA 85 A ALA 85 10 1_555 A THR 87 A THR 87 10 1_555 A ARG 92 A ARG 92 10 1_555 A TYR 105 A TYR 105 10 1_555 A SER 137 A SER 137 10 1_555 A ALA 138 A ALA 138 10 1_555 A VAL 139 A VAL 139 10 1_555 A TRP 193 A TRP 193 10 1_555 A ASP 194 A ASP 194 10 1_555 A GLU 93 A GLU 93 5 1_555 A VAL 96 A VAL 96 5 1_555 A ASP 97 A ASP 97 5 1_555 A HOH 2054 G HOH 5 1_555 A HOH 2114 G HOH 5 1_555 A LEU 11 A LEU 11 3 1_555 A VAL 52 A VAL 52 3 1_555 A HOH 2038 G HOH 3 1_555 A GLY 59 A GLY 59 4 1_555 A THR 89 A THR 89 4 1_555 A ARG 92 A ARG 92 4 1_555 A GLN 141 A GLN 141 4 1_555 A TYR 105 A TYR 105 4 1_555 A ALA 138 A ALA 138 4 1_555 A HIS 142 A HIS 142 4 1_555 A ARG 220 A ARG 220 4 1_555 1 P 1