data_6ZL5 # _model_server_result.job_id k-8PEFtxJ_wL0f7UwzXzdw _model_server_result.datetime_utc '2024-11-05 10:37:09' _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 6zl5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 6ZL5 # _exptl.entry_id 6ZL5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 6ZL5 _cell.length_a 83.802 _cell.length_b 83.802 _cell.length_c 87.416 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ZL5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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,F _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 3 _struct_asym.id C _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 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc2 B MG MG . A MG 201 1_555 C O3B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc3 B MG MG . A MG 201 1_555 F O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc4 B MG MG . A MG 201 1_555 F O HOH . A HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc5 B MG MG . A MG 201 1_555 F O HOH . A HOH 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc6 B MG MG . A MG 201 1_555 F O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? # _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 156 n n PB O2B GDP sing 157 n n PB O3B GDP sing 158 n n PB O3A GDP sing 159 n n O2B HOB2 GDP sing 160 n n O3B HOB3 GDP sing 161 n n O3A PA GDP sing 162 n n PA O1A GDP doub 163 n n PA O2A GDP sing 164 n n PA O5' GDP sing 165 n n O2A HOA2 GDP sing 166 n n O5' C5' GDP sing 167 n n C5' C4' GDP sing 168 n n C5' H5' GDP sing 169 n n C5' "H5''" GDP sing 170 n n C4' O4' GDP sing 171 n n C4' C3' GDP sing 172 n n C4' H4' GDP sing 173 n n O4' C1' GDP sing 174 n n C3' O3' GDP sing 175 n n C3' C2' GDP sing 176 n n C3' H3' GDP sing 177 n n O3' HO3' GDP sing 178 n n C2' O2' GDP sing 179 n n C2' C1' GDP sing 180 n n C2' H2' GDP sing 181 n n O2' HO2' GDP sing 182 n n C1' N9 GDP sing 183 n n C1' H1' GDP sing 184 n n N9 C8 GDP sing 185 n y N9 C4 GDP sing 186 n y C8 N7 GDP doub 187 n y C8 H8 GDP sing 188 n n N7 C5 GDP sing 189 n y C5 C6 GDP sing 190 n n C5 C4 GDP doub 191 n y C6 O6 GDP doub 192 n n C6 N1 GDP sing 193 n n N1 C2 GDP sing 194 n n N1 HN1 GDP sing 195 n n C2 N2 GDP sing 196 n n C2 N3 GDP doub 197 n n N2 HN21 GDP sing 198 n n N2 HN22 GDP sing 199 n n N3 C4 GDP sing 200 n n # _atom_sites.entry_id 6ZL5 _atom_sites.fract_transf_matrix[1][1] 0.011933 _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] 0.011933 _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] 0.01144 _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 MG A 1 201 1 MG MG . C 3 GDP A 1 202 1 GDP GDP . D 4 F0K A 1 203 1 F0K LIG . E 5 SO4 A 1 204 1 SO4 SO4 . F 6 HOH A 1 301 155 HOH HOH . F 6 HOH A 2 302 99 HOH HOH . F 6 HOH A 3 303 117 HOH HOH . F 6 HOH A 4 304 113 HOH HOH . F 6 HOH A 5 305 63 HOH HOH . F 6 HOH A 6 306 144 HOH HOH . F 6 HOH A 7 307 3 HOH HOH . F 6 HOH A 8 308 116 HOH HOH . F 6 HOH A 9 309 171 HOH HOH . F 6 HOH A 10 310 90 HOH HOH . F 6 HOH A 11 311 128 HOH HOH . F 6 HOH A 12 312 36 HOH HOH . F 6 HOH A 13 313 56 HOH HOH . F 6 HOH A 14 314 89 HOH HOH . F 6 HOH A 15 315 2 HOH HOH . F 6 HOH A 16 316 39 HOH HOH . F 6 HOH A 17 317 145 HOH HOH . F 6 HOH A 18 318 18 HOH HOH . F 6 HOH A 19 319 98 HOH HOH . F 6 HOH A 20 320 11 HOH HOH . F 6 HOH A 21 321 86 HOH HOH . F 6 HOH A 22 322 105 HOH HOH . F 6 HOH A 23 323 120 HOH HOH . F 6 HOH A 24 324 173 HOH HOH . F 6 HOH A 25 325 40 HOH HOH . F 6 HOH A 26 326 143 HOH HOH . F 6 HOH A 27 327 15 HOH HOH . F 6 HOH A 28 328 49 HOH HOH . F 6 HOH A 29 329 20 HOH HOH . F 6 HOH A 30 330 101 HOH HOH . F 6 HOH A 31 331 42 HOH HOH . F 6 HOH A 32 332 104 HOH HOH . F 6 HOH A 33 333 1 HOH HOH . F 6 HOH A 34 334 93 HOH HOH . F 6 HOH A 35 335 115 HOH HOH . F 6 HOH A 36 336 72 HOH HOH . F 6 HOH A 37 337 32 HOH HOH . F 6 HOH A 38 338 71 HOH HOH . F 6 HOH A 39 339 7 HOH HOH . F 6 HOH A 40 340 146 HOH HOH . F 6 HOH A 41 341 103 HOH HOH . F 6 HOH A 42 342 37 HOH HOH . F 6 HOH A 43 343 24 HOH HOH . F 6 HOH A 44 344 92 HOH HOH . F 6 HOH A 45 345 84 HOH HOH . F 6 HOH A 46 346 95 HOH HOH . F 6 HOH A 47 347 162 HOH HOH . F 6 HOH A 48 348 67 HOH HOH . F 6 HOH A 49 349 52 HOH HOH . F 6 HOH A 50 350 151 HOH HOH . F 6 HOH A 51 351 53 HOH HOH . F 6 HOH A 52 352 13 HOH HOH . F 6 HOH A 53 353 121 HOH HOH . F 6 HOH A 54 354 16 HOH HOH . F 6 HOH A 55 355 25 HOH HOH . F 6 HOH A 56 356 135 HOH HOH . F 6 HOH A 57 357 83 HOH HOH . F 6 HOH A 58 358 94 HOH HOH . F 6 HOH A 59 359 126 HOH HOH . F 6 HOH A 60 360 149 HOH HOH . F 6 HOH A 61 361 158 HOH HOH . F 6 HOH A 62 362 48 HOH HOH . F 6 HOH A 63 363 172 HOH HOH . F 6 HOH A 64 364 122 HOH HOH . F 6 HOH A 65 365 23 HOH HOH . F 6 HOH A 66 366 80 HOH HOH . F 6 HOH A 67 367 58 HOH HOH . F 6 HOH A 68 368 31 HOH HOH . F 6 HOH A 69 369 163 HOH HOH . F 6 HOH A 70 370 188 HOH HOH . F 6 HOH A 71 371 6 HOH HOH . F 6 HOH A 72 372 70 HOH HOH . F 6 HOH A 73 373 124 HOH HOH . F 6 HOH A 74 374 160 HOH HOH . F 6 HOH A 75 375 136 HOH HOH . F 6 HOH A 76 376 73 HOH HOH . F 6 HOH A 77 377 169 HOH HOH . F 6 HOH A 78 378 127 HOH HOH . F 6 HOH A 79 379 22 HOH HOH . F 6 HOH A 80 380 4 HOH HOH . F 6 HOH A 81 381 46 HOH HOH . F 6 HOH A 82 382 174 HOH HOH . F 6 HOH A 83 383 186 HOH HOH . F 6 HOH A 84 384 97 HOH HOH . F 6 HOH A 85 385 166 HOH HOH . F 6 HOH A 86 386 91 HOH HOH . F 6 HOH A 87 387 108 HOH HOH . F 6 HOH A 88 388 157 HOH HOH . F 6 HOH A 89 389 154 HOH HOH . F 6 HOH A 90 390 77 HOH HOH . F 6 HOH A 91 391 142 HOH HOH . F 6 HOH A 92 392 125 HOH HOH . F 6 HOH A 93 393 182 HOH HOH . F 6 HOH A 94 394 60 HOH HOH . F 6 HOH A 95 395 192 HOH HOH . F 6 HOH A 96 396 35 HOH HOH . F 6 HOH A 97 397 45 HOH HOH . F 6 HOH A 98 398 165 HOH HOH . F 6 HOH A 99 399 156 HOH HOH . F 6 HOH A 100 400 28 HOH HOH . F 6 HOH A 101 401 14 HOH HOH . F 6 HOH A 102 402 59 HOH HOH . F 6 HOH A 103 403 194 HOH HOH . F 6 HOH A 104 404 47 HOH HOH . F 6 HOH A 105 405 179 HOH HOH . F 6 HOH A 106 406 148 HOH HOH . F 6 HOH A 107 407 100 HOH HOH . F 6 HOH A 108 408 164 HOH HOH . F 6 HOH A 109 409 61 HOH HOH . F 6 HOH A 110 410 34 HOH HOH . F 6 HOH A 111 411 150 HOH HOH . F 6 HOH A 112 412 21 HOH HOH . F 6 HOH A 113 413 43 HOH HOH . F 6 HOH A 114 414 12 HOH HOH . F 6 HOH A 115 415 51 HOH HOH . F 6 HOH A 116 416 38 HOH HOH . F 6 HOH A 117 417 9 HOH HOH . F 6 HOH A 118 418 153 HOH HOH . F 6 HOH A 119 419 134 HOH HOH . F 6 HOH A 120 420 66 HOH HOH . F 6 HOH A 121 421 27 HOH HOH . F 6 HOH A 122 422 111 HOH HOH . F 6 HOH A 123 423 96 HOH HOH . F 6 HOH A 124 424 75 HOH HOH . F 6 HOH A 125 425 17 HOH HOH . F 6 HOH A 126 426 178 HOH HOH . F 6 HOH A 127 427 152 HOH HOH . F 6 HOH A 128 428 82 HOH HOH . F 6 HOH A 129 429 118 HOH HOH . F 6 HOH A 130 430 102 HOH HOH . F 6 HOH A 131 431 68 HOH HOH . F 6 HOH A 132 432 76 HOH HOH . F 6 HOH A 133 433 147 HOH HOH . F 6 HOH A 134 434 110 HOH HOH . F 6 HOH A 135 435 26 HOH HOH . F 6 HOH A 136 436 159 HOH HOH . F 6 HOH A 137 437 183 HOH HOH . F 6 HOH A 138 438 112 HOH HOH . F 6 HOH A 139 439 184 HOH HOH . F 6 HOH A 140 440 85 HOH HOH . F 6 HOH A 141 441 50 HOH HOH . F 6 HOH A 142 442 54 HOH HOH . F 6 HOH A 143 443 88 HOH HOH . F 6 HOH A 144 444 131 HOH HOH . F 6 HOH A 145 445 138 HOH HOH . F 6 HOH A 146 446 29 HOH HOH . F 6 HOH A 147 447 79 HOH HOH . F 6 HOH A 148 448 177 HOH HOH . F 6 HOH A 149 449 129 HOH HOH . F 6 HOH A 150 450 65 HOH HOH . F 6 HOH A 151 451 57 HOH HOH . F 6 HOH A 152 452 168 HOH HOH . F 6 HOH A 153 453 193 HOH HOH . F 6 HOH A 154 454 185 HOH HOH . F 6 HOH A 155 455 180 HOH HOH . F 6 HOH A 156 456 167 HOH HOH . F 6 HOH A 157 457 55 HOH HOH . F 6 HOH A 158 458 64 HOH HOH . F 6 HOH A 159 459 119 HOH HOH . F 6 HOH A 160 460 107 HOH HOH . F 6 HOH A 161 461 69 HOH HOH . F 6 HOH A 162 462 175 HOH HOH . F 6 HOH A 163 463 140 HOH HOH . F 6 HOH A 164 464 176 HOH HOH . F 6 HOH A 165 465 8 HOH HOH . F 6 HOH A 166 466 170 HOH HOH . F 6 HOH A 167 467 114 HOH HOH . F 6 HOH A 168 468 161 HOH HOH . F 6 HOH A 169 469 195 HOH HOH . F 6 HOH A 170 470 181 HOH HOH . F 6 HOH A 171 471 130 HOH HOH . F 6 HOH A 172 472 132 HOH HOH . F 6 HOH A 173 473 187 HOH HOH . F 6 HOH A 174 474 106 HOH HOH . F 6 HOH A 175 475 190 HOH HOH . F 6 HOH A 176 476 139 HOH HOH . F 6 HOH A 177 477 33 HOH HOH . F 6 HOH A 178 478 189 HOH HOH . F 6 HOH A 179 479 191 HOH HOH . F 6 HOH A 180 480 141 HOH HOH . F 6 HOH A 181 481 30 HOH HOH . F 6 HOH A 182 482 62 HOH HOH . F 6 HOH A 183 483 87 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 . . . C 3 -33.107 21.114 3.302 1 14.4 ? PB GDP 202 A 1 HETATM 2 O O1B GDP . . . C 3 -32.522 21.846 2.11 1 14.68 ? O1B GDP 202 A 1 HETATM 3 O O2B GDP . . . C 3 -32.854 19.629 3.092 1 14.02 ? O2B GDP 202 A 1 HETATM 4 O O3B GDP . . . C 3 -32.595 21.645 4.585 1 13.82 ? O3B GDP 202 A 1 HETATM 5 O O3A GDP . . . C 3 -34.686 21.283 3.178 1 14.69 ? O3A GDP 202 A 1 HETATM 6 P PA GDP . . . C 3 -35.692 22.26 3.934 1 15.3 ? PA GDP 202 A 1 HETATM 7 O O1A GDP . . . C 3 -35.187 23.672 3.731 1 15.54 ? O1A GDP 202 A 1 HETATM 8 O O2A GDP . . . C 3 -35.744 21.925 5.378 1 15.37 ? O2A GDP 202 A 1 HETATM 9 O O5' GDP . . . C 3 -37.069 22.009 3.176 1 15.33 ? O5' GDP 202 A 1 HETATM 10 C C5' GDP . . . C 3 -37.267 22.283 1.77 1 15.35 ? C5' GDP 202 A 1 HETATM 11 C C4' GDP . . . C 3 -38.736 22.543 1.539 1 15.69 ? C4' GDP 202 A 1 HETATM 12 O O4' GDP . . . C 3 -39.498 21.34 1.789 1 14.84 ? O4' GDP 202 A 1 HETATM 13 C C3' GDP . . . C 3 -39.364 23.625 2.419 1 16.49 ? C3' GDP 202 A 1 HETATM 14 O O3' GDP . . . C 3 -40.405 24.273 1.691 1 17.21 ? O3' GDP 202 A 1 HETATM 15 C C2' GDP . . . C 3 -39.955 22.811 3.572 1 15.6 ? C2' GDP 202 A 1 HETATM 16 O O2' GDP . . . C 3 -41.039 23.441 4.247 1 15.45 ? O2' GDP 202 A 1 HETATM 17 C C1' GDP . . . C 3 -40.438 21.573 2.823 1 14.83 ? C1' GDP 202 A 1 HETATM 18 N N9 GDP . . . C 3 -40.508 20.374 3.667 1 13.76 ? N9 GDP 202 A 1 HETATM 19 C C8 GDP . . . C 3 -39.513 19.865 4.46 1 13.17 ? C8 GDP 202 A 1 HETATM 20 N N7 GDP . . . C 3 -39.862 18.768 5.089 1 12.64 ? N7 GDP 202 A 1 HETATM 21 C C5 GDP . . . C 3 -41.163 18.537 4.679 1 12.83 ? C5 GDP 202 A 1 HETATM 22 C C6 GDP . . . C 3 -42.067 17.464 4.98 1 13.2 ? C6 GDP 202 A 1 HETATM 23 O O6 GDP . . . C 3 -41.859 16.498 5.72 1 12.88 ? O6 GDP 202 A 1 HETATM 24 N N1 GDP . . . C 3 -43.278 17.607 4.326 1 13.65 ? N1 GDP 202 A 1 HETATM 25 C C2 GDP . . . C 3 -43.603 18.653 3.493 1 13.74 ? C2 GDP 202 A 1 HETATM 26 N N2 GDP . . . C 3 -44.842 18.673 3.006 1 14.08 ? N2 GDP 202 A 1 HETATM 27 N N3 GDP . . . C 3 -42.768 19.647 3.199 1 13.27 ? N3 GDP 202 A 1 HETATM 28 C C4 GDP . . . C 3 -41.578 19.526 3.812 1 13.33 ? C4 GDP 202 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #