data_4EPX # _model_server_result.job_id UypKB7aq5iqmlPGXhVA4-g _model_server_result.datetime_utc '2024-11-14 11:00:15' _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 4epx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4EPX # _exptl.entry_id 4EPX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 4EPX _cell.length_a 39.132 _cell.length_b 41.473 _cell.length_c 91.726 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EPX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc2 B O1B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc3 C MG MG . A MG 202 1_555 E O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B GDP doub 112 n n PB O2B GDP sing 113 n n PB O3B GDP sing 114 n n PB O3A GDP sing 115 n n O2B HOB2 GDP sing 116 n n O3B HOB3 GDP sing 117 n n O3A PA GDP sing 118 n n PA O1A GDP doub 119 n n PA O2A GDP sing 120 n n PA O5' GDP sing 121 n n O2A HOA2 GDP sing 122 n n O5' C5' GDP sing 123 n n C5' C4' GDP sing 124 n n C5' H5' GDP sing 125 n n C5' "H5''" GDP sing 126 n n C4' O4' GDP sing 127 n n C4' C3' GDP sing 128 n n C4' H4' GDP sing 129 n n O4' C1' GDP sing 130 n n C3' O3' GDP sing 131 n n C3' C2' GDP sing 132 n n C3' H3' GDP sing 133 n n O3' HO3' GDP sing 134 n n C2' O2' GDP sing 135 n n C2' C1' GDP sing 136 n n C2' H2' GDP sing 137 n n O2' HO2' GDP sing 138 n n C1' N9 GDP sing 139 n n C1' H1' GDP sing 140 n n N9 C8 GDP sing 141 n y N9 C4 GDP sing 142 n y C8 N7 GDP doub 143 n y C8 H8 GDP sing 144 n n N7 C5 GDP sing 145 n y C5 C6 GDP sing 146 n n C5 C4 GDP doub 147 n y C6 O6 GDP doub 148 n n C6 N1 GDP sing 149 n n N1 C2 GDP sing 150 n n N1 HN1 GDP sing 151 n n C2 N2 GDP sing 152 n n C2 N3 GDP doub 153 n n N2 HN21 GDP sing 154 n n N2 HN22 GDP sing 155 n n N3 C4 GDP sing 156 n n # _atom_sites.entry_id 4EPX _atom_sites.fract_transf_matrix[1][1] 0.025555 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024112 _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] 0.010902 _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 B 2 GDP A 1 201 201 GDP GDP . C 3 MG A 1 202 1 MG MG . D 4 0QR A 1 203 1 0QR TKL . E 5 HOH A 1 301 1 HOH HOH . E 5 HOH A 2 302 2 HOH HOH . E 5 HOH A 3 303 3 HOH HOH . E 5 HOH A 4 304 4 HOH HOH . E 5 HOH A 5 305 5 HOH HOH . E 5 HOH A 6 306 6 HOH HOH . E 5 HOH A 7 307 7 HOH HOH . E 5 HOH A 8 308 8 HOH HOH . E 5 HOH A 9 309 9 HOH HOH . E 5 HOH A 10 310 10 HOH HOH . E 5 HOH A 11 311 11 HOH HOH . E 5 HOH A 12 312 12 HOH HOH . E 5 HOH A 13 313 13 HOH HOH . E 5 HOH A 14 314 14 HOH HOH . E 5 HOH A 15 315 15 HOH HOH . E 5 HOH A 16 316 16 HOH HOH . E 5 HOH A 17 317 17 HOH HOH . E 5 HOH A 18 318 18 HOH HOH . E 5 HOH A 19 319 19 HOH HOH . E 5 HOH A 20 320 20 HOH HOH . E 5 HOH A 21 321 21 HOH HOH . E 5 HOH A 22 322 22 HOH HOH . E 5 HOH A 23 323 23 HOH HOH . E 5 HOH A 24 324 24 HOH HOH . E 5 HOH A 25 325 25 HOH HOH . E 5 HOH A 26 326 26 HOH HOH . E 5 HOH A 27 327 27 HOH HOH . E 5 HOH A 28 328 28 HOH HOH . E 5 HOH A 29 329 29 HOH HOH . E 5 HOH A 30 330 30 HOH HOH . E 5 HOH A 31 331 31 HOH HOH . E 5 HOH A 32 332 32 HOH HOH . E 5 HOH A 33 333 33 HOH HOH . E 5 HOH A 34 334 34 HOH HOH . E 5 HOH A 35 335 35 HOH HOH . E 5 HOH A 36 336 36 HOH HOH . E 5 HOH A 37 337 37 HOH HOH . E 5 HOH A 38 338 38 HOH HOH . E 5 HOH A 39 339 39 HOH HOH . E 5 HOH A 40 340 40 HOH HOH . E 5 HOH A 41 341 41 HOH HOH . E 5 HOH A 42 342 42 HOH HOH . E 5 HOH A 43 343 43 HOH HOH . E 5 HOH A 44 344 44 HOH HOH . E 5 HOH A 45 345 45 HOH HOH . E 5 HOH A 46 346 46 HOH HOH . E 5 HOH A 47 347 47 HOH HOH . E 5 HOH A 48 348 48 HOH HOH . E 5 HOH A 49 349 49 HOH HOH . E 5 HOH A 50 350 50 HOH HOH . E 5 HOH A 51 351 51 HOH HOH . E 5 HOH A 52 352 52 HOH HOH . E 5 HOH A 53 353 53 HOH HOH . E 5 HOH A 54 354 54 HOH HOH . E 5 HOH A 55 355 55 HOH HOH . E 5 HOH A 56 356 56 HOH HOH . E 5 HOH A 57 357 57 HOH HOH . E 5 HOH A 58 358 58 HOH HOH . E 5 HOH A 59 359 59 HOH HOH . E 5 HOH A 60 360 60 HOH HOH . E 5 HOH A 61 361 61 HOH HOH . E 5 HOH A 62 362 62 HOH HOH . E 5 HOH A 63 363 63 HOH HOH . E 5 HOH A 64 364 64 HOH HOH . E 5 HOH A 65 365 65 HOH HOH . E 5 HOH A 66 366 66 HOH HOH . E 5 HOH A 67 367 67 HOH HOH . E 5 HOH A 68 368 68 HOH HOH . E 5 HOH A 69 369 70 HOH HOH . E 5 HOH A 70 370 71 HOH HOH . E 5 HOH A 71 371 72 HOH HOH . E 5 HOH A 72 372 73 HOH HOH . E 5 HOH A 73 373 74 HOH HOH . E 5 HOH A 74 374 75 HOH HOH . E 5 HOH A 75 375 76 HOH HOH . E 5 HOH A 76 376 77 HOH HOH . E 5 HOH A 77 377 78 HOH HOH . E 5 HOH A 78 378 79 HOH HOH . E 5 HOH A 79 379 80 HOH HOH . E 5 HOH A 80 380 81 HOH HOH . E 5 HOH A 81 381 82 HOH HOH . E 5 HOH A 82 382 83 HOH HOH . E 5 HOH A 83 383 85 HOH HOH . E 5 HOH A 84 384 86 HOH HOH . E 5 HOH A 85 385 87 HOH HOH . E 5 HOH A 86 386 88 HOH HOH . E 5 HOH A 87 387 89 HOH HOH . E 5 HOH A 88 388 90 HOH HOH . E 5 HOH A 89 389 92 HOH HOH . E 5 HOH A 90 390 93 HOH HOH . E 5 HOH A 91 391 94 HOH HOH . E 5 HOH A 92 392 95 HOH HOH . E 5 HOH A 93 393 96 HOH HOH . E 5 HOH A 94 394 97 HOH HOH . E 5 HOH A 95 395 99 HOH HOH . E 5 HOH A 96 396 100 HOH HOH . E 5 HOH A 97 397 101 HOH HOH . E 5 HOH A 98 398 102 HOH HOH . E 5 HOH A 99 399 103 HOH HOH . E 5 HOH A 100 400 104 HOH HOH . E 5 HOH A 101 401 105 HOH HOH . E 5 HOH A 102 402 106 HOH HOH . E 5 HOH A 103 403 107 HOH HOH . E 5 HOH A 104 404 108 HOH HOH . E 5 HOH A 105 405 109 HOH HOH . E 5 HOH A 106 406 110 HOH HOH . E 5 HOH A 107 407 111 HOH HOH . E 5 HOH A 108 408 112 HOH HOH . E 5 HOH A 109 409 113 HOH HOH . E 5 HOH A 110 410 115 HOH HOH . E 5 HOH A 111 411 116 HOH HOH . E 5 HOH A 112 412 117 HOH HOH . E 5 HOH A 113 413 118 HOH HOH . E 5 HOH A 114 414 121 HOH HOH . E 5 HOH A 115 415 123 HOH HOH . E 5 HOH A 116 416 124 HOH HOH . E 5 HOH A 117 417 125 HOH HOH . E 5 HOH A 118 418 126 HOH HOH . E 5 HOH A 119 419 127 HOH HOH . E 5 HOH A 120 420 128 HOH HOH . E 5 HOH A 121 421 131 HOH HOH . E 5 HOH A 122 422 134 HOH HOH . E 5 HOH A 123 423 135 HOH HOH . E 5 HOH A 124 424 136 HOH HOH . E 5 HOH A 125 425 137 HOH HOH . E 5 HOH A 126 426 138 HOH HOH . E 5 HOH A 127 427 139 HOH HOH . E 5 HOH A 128 428 140 HOH HOH . E 5 HOH A 129 429 141 HOH HOH . E 5 HOH A 130 430 142 HOH HOH . E 5 HOH A 131 431 143 HOH HOH . E 5 HOH A 132 432 145 HOH HOH . E 5 HOH A 133 433 146 HOH HOH . E 5 HOH A 134 434 147 HOH HOH . E 5 HOH A 135 435 148 HOH HOH . E 5 HOH A 136 436 149 HOH HOH . E 5 HOH A 137 437 150 HOH HOH . E 5 HOH A 138 438 151 HOH HOH . E 5 HOH A 139 439 152 HOH HOH . E 5 HOH A 140 440 153 HOH HOH . E 5 HOH A 141 441 154 HOH HOH . E 5 HOH A 142 442 156 HOH HOH . E 5 HOH A 143 443 157 HOH HOH . E 5 HOH A 144 444 159 HOH HOH . E 5 HOH A 145 445 160 HOH HOH . E 5 HOH A 146 446 161 HOH HOH . E 5 HOH A 147 447 162 HOH HOH . E 5 HOH A 148 448 163 HOH HOH . E 5 HOH A 149 449 164 HOH HOH . E 5 HOH A 150 450 166 HOH HOH . E 5 HOH A 151 451 167 HOH HOH . E 5 HOH A 152 452 168 HOH HOH . E 5 HOH A 153 453 169 HOH HOH . E 5 HOH A 154 454 170 HOH HOH . E 5 HOH A 155 455 172 HOH HOH . E 5 HOH A 156 456 173 HOH HOH . E 5 HOH A 157 457 175 HOH HOH . E 5 HOH A 158 458 176 HOH HOH . E 5 HOH A 159 459 178 HOH HOH . E 5 HOH A 160 460 179 HOH HOH . E 5 HOH A 161 461 181 HOH HOH . E 5 HOH A 162 462 182 HOH HOH . E 5 HOH A 163 463 183 HOH HOH . E 5 HOH A 164 464 184 HOH HOH . E 5 HOH A 165 465 185 HOH HOH . E 5 HOH A 166 466 186 HOH HOH . E 5 HOH A 167 467 187 HOH HOH . E 5 HOH A 168 468 188 HOH HOH . E 5 HOH A 169 469 189 HOH HOH . E 5 HOH A 170 470 190 HOH HOH . E 5 HOH A 171 471 191 HOH HOH . E 5 HOH A 172 472 192 HOH HOH . E 5 HOH A 173 473 193 HOH HOH . E 5 HOH A 174 474 194 HOH HOH . E 5 HOH A 175 475 195 HOH HOH . E 5 HOH A 176 476 196 HOH HOH . E 5 HOH A 177 477 197 HOH HOH . E 5 HOH A 178 478 198 HOH HOH . E 5 HOH A 179 479 199 HOH HOH . E 5 HOH A 180 480 200 HOH HOH . E 5 HOH A 181 481 201 HOH HOH . E 5 HOH A 182 482 202 HOH HOH . E 5 HOH A 183 483 203 HOH HOH . E 5 HOH A 184 484 204 HOH HOH . E 5 HOH A 185 485 205 HOH HOH . E 5 HOH A 186 486 206 HOH HOH . E 5 HOH A 187 487 207 HOH HOH . E 5 HOH A 188 488 208 HOH HOH . E 5 HOH A 189 489 209 HOH HOH . E 5 HOH A 190 490 210 HOH HOH . E 5 HOH A 191 491 211 HOH HOH . E 5 HOH A 192 492 212 HOH HOH . E 5 HOH A 193 493 213 HOH HOH . E 5 HOH A 194 494 214 HOH HOH . E 5 HOH A 195 495 215 HOH HOH . E 5 HOH A 196 496 216 HOH HOH . E 5 HOH A 197 497 217 HOH HOH . E 5 HOH A 198 498 218 HOH HOH . E 5 HOH A 199 499 219 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB GDP . . . B 2 10.09 -7.423 16.25 1 13.89 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 11.189 -7.757 15.226 1 11.02 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 9.85 -5.931 16.306 1 12.33 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 10.467 -7.927 17.61 1 14.32 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 8.726 -8.185 15.844 1 12.87 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 8.533 -9.41 14.887 1 13.69 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 8.672 -9.031 13.458 1 12.35 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 9.389 -10.511 15.406 1 15.76 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 6.954 -9.7 15.095 1 13.89 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 6.519 -10.023 16.447 1 14.44 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 5.271 -10.893 16.294 1 16.66 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 4.241 -10.102 15.653 1 14.62 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 5.548 -12.054 15.349 1 17.44 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 4.736 -13.119 15.858 1 20.79 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 5.002 -11.611 13.993 1 18.11 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 4.412 -12.645 13.204 1 24.1 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 3.865 -10.715 14.403 1 15.41 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 3.609 -9.632 13.462 1 12.42 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 4.552 -8.76 13.005 1 10.62 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 3.983 -7.881 12.151 1 11.84 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 2.634 -8.171 12.101 1 12.63 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 1.475 -7.671 11.398 1 14.48 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 1.541 -6.673 10.67 1 14.34 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 0.283 -8.244 11.608 1 15.87 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 0.121 -9.342 12.394 1 18.96 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -1.128 -9.876 12.536 1 20.7 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 1.146 -9.891 13.072 1 14.87 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 2.417 -9.358 12.943 1 13.45 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #