data_4YHQ # _model_server_result.job_id DNJYm1FAMRjEi3J6oficoA _model_server_result.datetime_utc '2024-11-22 04:36:09' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4yhq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 4YHQ # _exptl.entry_id 4YHQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 88.906 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'YTTRIUM ION' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 4YHQ _cell.length_a 60.303 _cell.length_b 60.303 _cell.length_c 86.141 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YHQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 K N N ? 3 L N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.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.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OD1 ASP 35 A ASP 35 1_555 D Y Y1 . A Y1 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc2 A OD2 ASP 35 A ASP 35 1_555 D Y Y1 . A Y1 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc3 A OD2 ASP 35 A ASP 35 1_555 E Y Y1 . A Y1 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc4 A OE2 GLU 58 A GLU 58 1_555 D Y Y1 . A Y1 202 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc5 A OE2 GLU 58 A GLU 58 1_555 E Y Y1 . A Y1 203 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc6 A OD1 ASP 60 A ASP 60 1_555 D Y Y1 . A Y1 202 6_555 ? A ? ? ? ? ? ? ? ? ? ? 2.978 ? metalc ? metalc7 A OD2 ASP 60 A ASP 60 1_555 D Y Y1 . A Y1 202 6_555 ? A ? ? ? ? ? ? ? ? ? ? 3.111 ? metalc ? metalc8 A OD1 ASP 60 A ASP 60 1_555 E Y Y1 . A Y1 203 6_555 ? A ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc9 A OD2 ASP 60 A ASP 60 1_555 E Y Y1 . A Y1 203 6_555 ? A ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc10 A OG1 THR 89 A THR 89 1_555 I NA NA . A NA 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc11 D Y Y1 . A Y1 202 1_555 P O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.204 ? metalc ? metalc12 D Y Y1 . A Y1 202 1_555 P O HOH . A HOH 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc13 I NA NA . A NA 207 1_555 P O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc14 I NA NA . A NA 207 1_555 P O HOH . A HOH 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.134 ? metalc ? metalc15 B OD1 ASP 35 B ASP 35 1_555 K Y Y1 . B Y1 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc16 B OD2 ASP 35 B ASP 35 1_555 K Y Y1 . B Y1 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc17 B OD1 ASP 35 B ASP 35 1_555 L Y Y1 . B Y1 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc18 B NZ LYS 43 B LYS 43 1_555 K Y Y1 . B Y1 101 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 3.407 ? metalc ? metalc19 B NZ LYS 43 B LYS 43 1_555 L Y Y1 . B Y1 102 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc20 B OE2 GLU 58 B GLU 58 1_555 K Y Y1 . B Y1 101 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc21 B OE1 GLU 58 B GLU 58 1_555 L Y Y1 . B Y1 102 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 3.422 ? metalc ? metalc22 B OE2 GLU 58 B GLU 58 1_555 L Y Y1 . B Y1 102 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc23 B OD1 ASP 60 B ASP 60 1_555 K Y Y1 . B Y1 101 5_554 ? A ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc24 B OD1 ASP 60 B ASP 60 1_555 L Y Y1 . B Y1 102 5_554 ? A ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc25 B OD2 ASP 60 B ASP 60 1_555 L Y Y1 . B Y1 102 5_554 ? A ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc26 K Y Y1 . B Y1 101 1_555 Q O HOH . B HOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.207 ? metalc ? metalc27 K Y Y1 . B Y1 101 1_555 Q O HOH . B HOH 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc28 K Y Y1 . B Y1 101 1_555 Q O HOH . B HOH 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc29 L Y Y1 . B Y1 102 1_555 Q O HOH . B HOH 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? # _chem_comp.formula 'Y 2' _chem_comp.formula_weight 88.906 _chem_comp.id Y1 _chem_comp.mon_nstd_flag . _chem_comp.name 'YTTRIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4YHQ _atom_sites.fract_transf_matrix[1][1] 0.016583 _atom_sites.fract_transf_matrix[1][2] 0.009574 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019148 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011609 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 G10 A 1 201 201 G10 G10 . D 3 Y1 A 1 202 1 Y1 Y1 . E 3 Y1 A 1 203 3 Y1 Y1 . F 4 CL A 1 204 5 CL CL . G 4 CL A 1 205 6 CL CL . H 4 CL A 1 206 9 CL CL . I 5 NA A 1 207 10 NA NA . J 6 GOL A 1 208 22 GOL GOL . K 3 Y1 B 1 101 2 Y1 Y1 . L 3 Y1 B 1 102 4 Y1 Y1 . M 4 CL B 1 103 7 CL CL . N 4 CL B 1 104 8 CL CL . O 6 GOL B 1 105 21 GOL GOL . P 7 HOH A 1 301 155 HOH HOH . P 7 HOH A 2 302 87 HOH HOH . P 7 HOH A 3 303 126 HOH HOH . P 7 HOH A 4 304 129 HOH HOH . P 7 HOH A 5 305 31 HOH HOH . P 7 HOH A 6 306 167 HOH HOH . P 7 HOH A 7 307 158 HOH HOH . P 7 HOH A 8 308 90 HOH HOH . P 7 HOH A 9 309 163 HOH HOH . P 7 HOH A 10 310 17 HOH HOH . P 7 HOH A 11 311 37 HOH HOH . P 7 HOH A 12 312 60 HOH HOH . P 7 HOH A 13 313 143 HOH HOH . P 7 HOH A 14 314 63 HOH HOH . P 7 HOH A 15 315 57 HOH HOH . P 7 HOH A 16 316 73 HOH HOH . P 7 HOH A 17 317 74 HOH HOH . P 7 HOH A 18 318 146 HOH HOH . P 7 HOH A 19 319 99 HOH HOH . P 7 HOH A 20 320 58 HOH HOH . P 7 HOH A 21 321 78 HOH HOH . P 7 HOH A 22 322 32 HOH HOH . P 7 HOH A 23 323 30 HOH HOH . P 7 HOH A 24 324 69 HOH HOH . P 7 HOH A 25 325 1 HOH HOH . P 7 HOH A 26 326 25 HOH HOH . P 7 HOH A 27 327 109 HOH HOH . P 7 HOH A 28 328 93 HOH HOH . P 7 HOH A 29 329 42 HOH HOH . P 7 HOH A 30 330 111 HOH HOH . P 7 HOH A 31 331 21 HOH HOH . P 7 HOH A 32 332 18 HOH HOH . P 7 HOH A 33 333 75 HOH HOH . P 7 HOH A 34 334 89 HOH HOH . P 7 HOH A 35 335 133 HOH HOH . P 7 HOH A 36 336 170 HOH HOH . P 7 HOH A 37 337 85 HOH HOH . P 7 HOH A 38 338 68 HOH HOH . P 7 HOH A 39 339 45 HOH HOH . P 7 HOH A 40 340 35 HOH HOH . P 7 HOH A 41 341 56 HOH HOH . P 7 HOH A 42 342 4 HOH HOH . P 7 HOH A 43 343 33 HOH HOH . P 7 HOH A 44 344 135 HOH HOH . P 7 HOH A 45 345 29 HOH HOH . P 7 HOH A 46 346 159 HOH HOH . P 7 HOH A 47 347 145 HOH HOH . P 7 HOH A 48 348 55 HOH HOH . P 7 HOH A 49 349 101 HOH HOH . P 7 HOH A 50 350 19 HOH HOH . P 7 HOH A 51 351 108 HOH HOH . P 7 HOH A 52 352 77 HOH HOH . P 7 HOH A 53 353 95 HOH HOH . P 7 HOH A 54 354 144 HOH HOH . P 7 HOH A 55 355 62 HOH HOH . P 7 HOH A 56 356 148 HOH HOH . P 7 HOH A 57 357 94 HOH HOH . P 7 HOH A 58 358 12 HOH HOH . P 7 HOH A 59 359 147 HOH HOH . P 7 HOH A 60 360 27 HOH HOH . P 7 HOH A 61 361 107 HOH HOH . P 7 HOH A 62 362 175 HOH HOH . P 7 HOH A 63 363 88 HOH HOH . P 7 HOH A 64 364 81 HOH HOH . P 7 HOH A 65 365 96 HOH HOH . P 7 HOH A 66 366 171 HOH HOH . P 7 HOH A 67 367 5 HOH HOH . P 7 HOH A 68 368 71 HOH HOH . P 7 HOH A 69 369 142 HOH HOH . P 7 HOH A 70 370 16 HOH HOH . P 7 HOH A 71 371 6 HOH HOH . P 7 HOH A 72 372 120 HOH HOH . P 7 HOH A 73 373 48 HOH HOH . P 7 HOH A 74 374 141 HOH HOH . P 7 HOH A 75 375 14 HOH HOH . P 7 HOH A 76 376 139 HOH HOH . P 7 HOH A 77 377 149 HOH HOH . P 7 HOH A 78 378 59 HOH HOH . P 7 HOH A 79 379 161 HOH HOH . P 7 HOH A 80 380 150 HOH HOH . P 7 HOH A 81 381 97 HOH HOH . P 7 HOH A 82 382 160 HOH HOH . P 7 HOH A 83 383 91 HOH HOH . P 7 HOH A 84 384 66 HOH HOH . P 7 HOH A 85 385 39 HOH HOH . P 7 HOH A 86 386 157 HOH HOH . P 7 HOH A 87 387 112 HOH HOH . P 7 HOH A 88 388 70 HOH HOH . P 7 HOH A 89 389 168 HOH HOH . Q 7 HOH B 1 201 123 HOH HOH . Q 7 HOH B 2 202 128 HOH HOH . Q 7 HOH B 3 203 44 HOH HOH . Q 7 HOH B 4 204 134 HOH HOH . Q 7 HOH B 5 205 124 HOH HOH . Q 7 HOH B 6 206 105 HOH HOH . Q 7 HOH B 7 207 8 HOH HOH . Q 7 HOH B 8 208 43 HOH HOH . Q 7 HOH B 9 209 54 HOH HOH . Q 7 HOH B 10 210 151 HOH HOH . Q 7 HOH B 11 211 154 HOH HOH . Q 7 HOH B 12 212 127 HOH HOH . Q 7 HOH B 13 213 84 HOH HOH . Q 7 HOH B 14 214 136 HOH HOH . Q 7 HOH B 15 215 98 HOH HOH . Q 7 HOH B 16 216 115 HOH HOH . Q 7 HOH B 17 217 67 HOH HOH . Q 7 HOH B 18 218 51 HOH HOH . Q 7 HOH B 19 219 165 HOH HOH . Q 7 HOH B 20 220 36 HOH HOH . Q 7 HOH B 21 221 41 HOH HOH . Q 7 HOH B 22 222 140 HOH HOH . Q 7 HOH B 23 223 83 HOH HOH . Q 7 HOH B 24 224 80 HOH HOH . Q 7 HOH B 25 225 86 HOH HOH . Q 7 HOH B 26 226 7 HOH HOH . Q 7 HOH B 27 227 3 HOH HOH . Q 7 HOH B 28 228 22 HOH HOH . Q 7 HOH B 29 229 50 HOH HOH . Q 7 HOH B 30 230 15 HOH HOH . Q 7 HOH B 31 231 116 HOH HOH . Q 7 HOH B 32 232 40 HOH HOH . Q 7 HOH B 33 233 24 HOH HOH . Q 7 HOH B 34 234 156 HOH HOH . Q 7 HOH B 35 235 47 HOH HOH . Q 7 HOH B 36 236 9 HOH HOH . Q 7 HOH B 37 237 38 HOH HOH . Q 7 HOH B 38 238 61 HOH HOH . Q 7 HOH B 39 239 119 HOH HOH . Q 7 HOH B 40 240 13 HOH HOH . Q 7 HOH B 41 241 103 HOH HOH . Q 7 HOH B 42 242 72 HOH HOH . Q 7 HOH B 43 243 113 HOH HOH . Q 7 HOH B 44 244 102 HOH HOH . Q 7 HOH B 45 245 20 HOH HOH . Q 7 HOH B 46 246 110 HOH HOH . Q 7 HOH B 47 247 174 HOH HOH . Q 7 HOH B 48 248 106 HOH HOH . Q 7 HOH B 49 249 104 HOH HOH . Q 7 HOH B 50 250 79 HOH HOH . Q 7 HOH B 51 251 118 HOH HOH . Q 7 HOH B 52 252 28 HOH HOH . Q 7 HOH B 53 253 132 HOH HOH . Q 7 HOH B 54 254 26 HOH HOH . Q 7 HOH B 55 255 23 HOH HOH . Q 7 HOH B 56 256 64 HOH HOH . Q 7 HOH B 57 257 2 HOH HOH . Q 7 HOH B 58 258 52 HOH HOH . Q 7 HOH B 59 259 49 HOH HOH . Q 7 HOH B 60 260 10 HOH HOH . Q 7 HOH B 61 261 11 HOH HOH . Q 7 HOH B 62 262 34 HOH HOH . Q 7 HOH B 63 263 76 HOH HOH . Q 7 HOH B 64 264 46 HOH HOH . Q 7 HOH B 65 265 162 HOH HOH . Q 7 HOH B 66 266 100 HOH HOH . Q 7 HOH B 67 267 131 HOH HOH . Q 7 HOH B 68 268 92 HOH HOH . Q 7 HOH B 69 269 138 HOH HOH . Q 7 HOH B 70 270 53 HOH HOH . Q 7 HOH B 71 271 166 HOH HOH . Q 7 HOH B 72 272 172 HOH HOH . Q 7 HOH B 73 273 153 HOH HOH . Q 7 HOH B 74 274 117 HOH HOH . Q 7 HOH B 75 275 152 HOH HOH . Q 7 HOH B 76 276 114 HOH HOH . Q 7 HOH B 77 277 164 HOH HOH . Q 7 HOH B 78 278 122 HOH HOH . Q 7 HOH B 79 279 130 HOH HOH . Q 7 HOH B 80 280 65 HOH HOH . Q 7 HOH B 81 281 169 HOH HOH . Q 7 HOH B 82 282 82 HOH HOH . Q 7 HOH B 83 283 121 HOH HOH . Q 7 HOH B 84 284 173 HOH HOH . Q 7 HOH B 85 285 137 HOH HOH . Q 7 HOH B 86 286 125 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol Y _atom_site.label_atom_id Y _atom_site.label_comp_id Y1 _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 3 _atom_site.Cartn_x -9.778 _atom_site.Cartn_y 15.372 _atom_site.Cartn_z 7.545 _atom_site.occupancy 0.3 _atom_site.B_iso_or_equiv 23.73 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id Y _atom_site.auth_comp_id Y1 _atom_site.auth_seq_id 202 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #