data_6V6V # _model_server_result.job_id pKrkWR7M1WBg-TmqJr94Sw _model_server_result.datetime_utc '2024-11-25 07:28:44' _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 6v6v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6V6V # _exptl.entry_id 6V6V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method nat _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 95.2 _cell.angle_gamma 90 _cell.entry_id 6V6V _cell.length_a 32.225 _cell.length_b 86.924 _cell.length_c 34.078 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6V6V _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 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 OG1 THR 21 A THR 19 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc2 A O PRO 38 A PRO 36 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc3 B O3B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc4 C MG MG . A MG 202 1_555 F O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc5 C MG MG . A MG 202 1_555 F O HOH . A HOH 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc6 C MG MG . A MG 202 1_555 F O HOH . A HOH 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? # _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 97 n n PB O2B GDP sing 98 n n PB O3B GDP sing 99 n n PB O3A GDP sing 100 n n O2B HOB2 GDP sing 101 n n O3B HOB3 GDP sing 102 n n O3A PA GDP sing 103 n n PA O1A GDP doub 104 n n PA O2A GDP sing 105 n n PA O5' GDP sing 106 n n O2A HOA2 GDP sing 107 n n O5' C5' GDP sing 108 n n C5' C4' GDP sing 109 n n C5' H5' GDP sing 110 n n C5' "H5''" GDP sing 111 n n C4' O4' GDP sing 112 n n C4' C3' GDP sing 113 n n C4' H4' GDP sing 114 n n O4' C1' GDP sing 115 n n C3' O3' GDP sing 116 n n C3' C2' GDP sing 117 n n C3' H3' GDP sing 118 n n O3' HO3' GDP sing 119 n n C2' O2' GDP sing 120 n n C2' C1' GDP sing 121 n n C2' H2' GDP sing 122 n n O2' HO2' GDP sing 123 n n C1' N9 GDP sing 124 n n C1' H1' GDP sing 125 n n N9 C8 GDP sing 126 n y N9 C4 GDP sing 127 n y C8 N7 GDP doub 128 n y C8 H8 GDP sing 129 n n N7 C5 GDP sing 130 n y C5 C6 GDP sing 131 n n C5 C4 GDP doub 132 n y C6 O6 GDP doub 133 n n C6 N1 GDP sing 134 n n N1 C2 GDP sing 135 n n N1 HN1 GDP sing 136 n n C2 N2 GDP sing 137 n n C2 N3 GDP doub 138 n n N2 HN21 GDP sing 139 n n N2 HN22 GDP sing 140 n n N3 C4 GDP sing 141 n n # _atom_sites.entry_id 6V6V _atom_sites.fract_transf_matrix[1][1] 0.031032 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002824 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011504 _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] 0.029466 _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 1 201 200 GDP GDP . C 3 MG A 1 202 300 MG MG . D 4 DIO A 1 203 1 DIO DIO . E 4 DIO A 1 204 2 DIO DIO . F 5 HOH A 1 301 120 HOH HOH . F 5 HOH A 2 302 169 HOH HOH . F 5 HOH A 3 303 152 HOH HOH . F 5 HOH A 4 304 37 HOH HOH . F 5 HOH A 5 305 73 HOH HOH . F 5 HOH A 6 306 109 HOH HOH . F 5 HOH A 7 307 157 HOH HOH . F 5 HOH A 8 308 52 HOH HOH . F 5 HOH A 9 309 51 HOH HOH . F 5 HOH A 10 310 99 HOH HOH . F 5 HOH A 11 311 127 HOH HOH . F 5 HOH A 12 312 5 HOH HOH . F 5 HOH A 13 313 118 HOH HOH . F 5 HOH A 14 314 166 HOH HOH . F 5 HOH A 15 315 90 HOH HOH . F 5 HOH A 16 316 81 HOH HOH . F 5 HOH A 17 317 69 HOH HOH . F 5 HOH A 18 318 96 HOH HOH . F 5 HOH A 19 319 55 HOH HOH . F 5 HOH A 20 320 112 HOH HOH . F 5 HOH A 21 321 60 HOH HOH . F 5 HOH A 22 322 168 HOH HOH . F 5 HOH A 23 323 8 HOH HOH . F 5 HOH A 24 324 40 HOH HOH . F 5 HOH A 25 325 126 HOH HOH . F 5 HOH A 26 326 32 HOH HOH . F 5 HOH A 27 327 22 HOH HOH . F 5 HOH A 28 328 95 HOH HOH . F 5 HOH A 29 329 119 HOH HOH . F 5 HOH A 30 330 106 HOH HOH . F 5 HOH A 31 331 111 HOH HOH . F 5 HOH A 32 332 88 HOH HOH . F 5 HOH A 33 333 3 HOH HOH . F 5 HOH A 34 334 29 HOH HOH . F 5 HOH A 35 335 9 HOH HOH . F 5 HOH A 36 336 172 HOH HOH . F 5 HOH A 37 337 48 HOH HOH . F 5 HOH A 38 338 14 HOH HOH . F 5 HOH A 39 339 42 HOH HOH . F 5 HOH A 40 340 77 HOH HOH . F 5 HOH A 41 341 15 HOH HOH . F 5 HOH A 42 342 11 HOH HOH . F 5 HOH A 43 343 24 HOH HOH . F 5 HOH A 44 344 84 HOH HOH . F 5 HOH A 45 345 66 HOH HOH . F 5 HOH A 46 346 18 HOH HOH . F 5 HOH A 47 347 1 HOH HOH . F 5 HOH A 48 348 4 HOH HOH . F 5 HOH A 49 349 92 HOH HOH . F 5 HOH A 50 350 153 HOH HOH . F 5 HOH A 51 351 30 HOH HOH . F 5 HOH A 52 352 25 HOH HOH . F 5 HOH A 53 353 13 HOH HOH . F 5 HOH A 54 354 31 HOH HOH . F 5 HOH A 55 355 7 HOH HOH . F 5 HOH A 56 356 101 HOH HOH . F 5 HOH A 57 357 83 HOH HOH . F 5 HOH A 58 358 117 HOH HOH . F 5 HOH A 59 359 108 HOH HOH . F 5 HOH A 60 360 46 HOH HOH . F 5 HOH A 61 361 162 HOH HOH . F 5 HOH A 62 362 19 HOH HOH . F 5 HOH A 63 363 41 HOH HOH . F 5 HOH A 64 364 53 HOH HOH . F 5 HOH A 65 365 137 HOH HOH . F 5 HOH A 66 366 159 HOH HOH . F 5 HOH A 67 367 91 HOH HOH . F 5 HOH A 68 368 100 HOH HOH . F 5 HOH A 69 369 102 HOH HOH . F 5 HOH A 70 370 121 HOH HOH . F 5 HOH A 71 371 35 HOH HOH . F 5 HOH A 72 372 114 HOH HOH . F 5 HOH A 73 373 39 HOH HOH . F 5 HOH A 74 374 43 HOH HOH . F 5 HOH A 75 375 75 HOH HOH . F 5 HOH A 76 376 38 HOH HOH . F 5 HOH A 77 377 61 HOH HOH . F 5 HOH A 78 378 6 HOH HOH . F 5 HOH A 79 379 62 HOH HOH . F 5 HOH A 80 380 136 HOH HOH . F 5 HOH A 81 381 2 HOH HOH . F 5 HOH A 82 382 67 HOH HOH . F 5 HOH A 83 383 128 HOH HOH . F 5 HOH A 84 384 17 HOH HOH . F 5 HOH A 85 385 50 HOH HOH . F 5 HOH A 86 386 34 HOH HOH . F 5 HOH A 87 387 26 HOH HOH . F 5 HOH A 88 388 12 HOH HOH . F 5 HOH A 89 389 164 HOH HOH . F 5 HOH A 90 390 10 HOH HOH . F 5 HOH A 91 391 21 HOH HOH . F 5 HOH A 92 392 167 HOH HOH . F 5 HOH A 93 393 94 HOH HOH . F 5 HOH A 94 394 36 HOH HOH . F 5 HOH A 95 395 33 HOH HOH . F 5 HOH A 96 396 28 HOH HOH . F 5 HOH A 97 397 170 HOH HOH . F 5 HOH A 98 398 146 HOH HOH . F 5 HOH A 99 399 129 HOH HOH . F 5 HOH A 100 400 110 HOH HOH . F 5 HOH A 101 401 161 HOH HOH . F 5 HOH A 102 402 131 HOH HOH . F 5 HOH A 103 403 143 HOH HOH . F 5 HOH A 104 404 20 HOH HOH . F 5 HOH A 105 405 23 HOH HOH . F 5 HOH A 106 406 64 HOH HOH . F 5 HOH A 107 407 56 HOH HOH . F 5 HOH A 108 408 134 HOH HOH . F 5 HOH A 109 409 97 HOH HOH . F 5 HOH A 110 410 154 HOH HOH . F 5 HOH A 111 411 107 HOH HOH . F 5 HOH A 112 412 138 HOH HOH . F 5 HOH A 113 413 80 HOH HOH . F 5 HOH A 114 414 45 HOH HOH . F 5 HOH A 115 415 86 HOH HOH . F 5 HOH A 116 416 140 HOH HOH . F 5 HOH A 117 417 125 HOH HOH . F 5 HOH A 118 418 145 HOH HOH . F 5 HOH A 119 419 105 HOH HOH . F 5 HOH A 120 420 71 HOH HOH . F 5 HOH A 121 421 116 HOH HOH . F 5 HOH A 122 422 130 HOH HOH . F 5 HOH A 123 423 76 HOH HOH . F 5 HOH A 124 424 87 HOH HOH . F 5 HOH A 125 425 177 HOH HOH . F 5 HOH A 126 426 135 HOH HOH . F 5 HOH A 127 427 93 HOH HOH . F 5 HOH A 128 428 103 HOH HOH . F 5 HOH A 129 429 176 HOH HOH . F 5 HOH A 130 430 47 HOH HOH . F 5 HOH A 131 431 98 HOH HOH . F 5 HOH A 132 432 59 HOH HOH . F 5 HOH A 133 433 82 HOH HOH . F 5 HOH A 134 434 72 HOH HOH . F 5 HOH A 135 435 44 HOH HOH . F 5 HOH A 136 436 124 HOH HOH . F 5 HOH A 137 437 139 HOH HOH . F 5 HOH A 138 438 78 HOH HOH . F 5 HOH A 139 439 174 HOH HOH . F 5 HOH A 140 440 158 HOH HOH . F 5 HOH A 141 441 160 HOH HOH . F 5 HOH A 142 442 104 HOH HOH . F 5 HOH A 143 443 89 HOH HOH . F 5 HOH A 144 444 142 HOH HOH . F 5 HOH A 145 445 163 HOH HOH . F 5 HOH A 146 446 65 HOH HOH . F 5 HOH A 147 447 175 HOH HOH . F 5 HOH A 148 448 165 HOH HOH . F 5 HOH A 149 449 115 HOH HOH . F 5 HOH A 150 450 54 HOH HOH . F 5 HOH A 151 451 79 HOH HOH . F 5 HOH A 152 452 74 HOH HOH . F 5 HOH A 153 453 156 HOH HOH . F 5 HOH A 154 454 141 HOH HOH . F 5 HOH A 155 455 57 HOH HOH . F 5 HOH A 156 456 122 HOH HOH . F 5 HOH A 157 457 147 HOH HOH . F 5 HOH A 158 458 148 HOH HOH . F 5 HOH A 159 459 155 HOH HOH . F 5 HOH A 160 460 27 HOH HOH . F 5 HOH A 161 461 144 HOH HOH . F 5 HOH A 162 462 63 HOH HOH . F 5 HOH A 163 463 151 HOH HOH . F 5 HOH A 164 464 123 HOH HOH . F 5 HOH A 165 465 178 HOH HOH . F 5 HOH A 166 466 85 HOH HOH . F 5 HOH A 167 467 149 HOH HOH . F 5 HOH A 168 468 132 HOH HOH . F 5 HOH A 169 469 68 HOH HOH . F 5 HOH A 170 470 49 HOH HOH . F 5 HOH A 171 471 173 HOH HOH . F 5 HOH A 172 472 16 HOH HOH . F 5 HOH A 173 473 150 HOH HOH . F 5 HOH A 174 474 113 HOH HOH . F 5 HOH A 175 475 70 HOH HOH . F 5 HOH A 176 476 171 HOH HOH . F 5 HOH A 177 477 58 HOH HOH . F 5 HOH A 178 478 133 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 -4.662 0.37 1.888 1 12.41 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -5.606 -0.366 0.968 1 14.82 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -3.211 0.249 1.497 1 12.43 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -5.053 1.813 2.096 1 13.51 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -4.744 -0.38 3.351 1 11.66 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -5.558 0.078 4.662 1 13.69 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -4.834 1.212 5.332 1 14.86 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -7.016 0.296 4.409 1 13.58 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -5.394 -1.214 5.621 1 12.54 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -5.89 -2.475 5.169 1 15.67 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -6.136 -3.383 6.363 1 16.7 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -4.904 -3.561 7.043 1 13.24 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -7.101 -2.803 7.376 1 20.7 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -7.915 -3.875 7.886 1 23.87 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -6.218 -2.309 8.499 1 21.82 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -6.884 -2.383 9.758 1 26.55 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -5.053 -3.277 8.435 1 15.54 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -3.811 -2.613 8.861 1 14.01 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -3.329 -1.433 8.375 1 13.98 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -2.127 -1.141 8.943 1 14.24 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -1.829 -2.15 9.793 1 15.69 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -0.721 -2.474 10.715 1 14.61 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 0.274 -1.727 10.863 1 13.25 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -0.809 -3.631 11.385 1 12.76 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -1.852 -4.482 11.276 1 15.78 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -1.851 -5.629 12.001 1 15.99 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -2.9 -4.26 10.448 1 13.6 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -2.933 -3.116 9.719 1 12.56 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #