data_6E6G # _model_server_result.job_id 0_W2wd2H8PU6o7yhibMs6w _model_server_result.datetime_utc '2024-11-28 15:20:54' _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 6e6g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6E6G # _exptl.entry_id 6E6G _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 6E6G _cell.length_a 36.096 _cell.length_b 37.829 _cell.length_c 100.171 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6E6G _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 OD1 ASP 13 A ASP 13 1_555 D NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc2 A O GLN 22 A GLN 22 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc3 A O LEU 23 A LEU 23 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc4 A OD1 ASN 26 A ASN 26 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc5 B O3B GDP . A GDP 201 1_555 D NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.949 ? metalc ? metalc6 C CA CA . A CA 202 1_555 E O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc7 C CA CA . A CA 202 1_555 E O HOH . A HOH 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc8 C CA CA . A CA 202 1_555 E O HOH . A HOH 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc9 D NA NA . A NA 203 1_555 E O HOH . A HOH 373 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc10 D NA NA . A NA 203 1_555 E O HOH . A HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 6E6G _atom_sites.fract_transf_matrix[1][1] 0.027704 _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] 0.026435 _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] 0.009983 _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 CA A 1 202 202 CA CA . D 4 NA A 1 203 203 NA NA . E 5 HOH A 1 301 104 HOH HOH . E 5 HOH A 2 302 138 HOH HOH . E 5 HOH A 3 303 89 HOH HOH . E 5 HOH A 4 304 53 HOH HOH . E 5 HOH A 5 305 100 HOH HOH . E 5 HOH A 6 306 149 HOH HOH . E 5 HOH A 7 307 86 HOH HOH . E 5 HOH A 8 308 65 HOH HOH . E 5 HOH A 9 309 66 HOH HOH . E 5 HOH A 10 310 12 HOH HOH . E 5 HOH A 11 311 130 HOH HOH . E 5 HOH A 12 312 13 HOH HOH . E 5 HOH A 13 313 25 HOH HOH . E 5 HOH A 14 314 67 HOH HOH . E 5 HOH A 15 315 106 HOH HOH . E 5 HOH A 16 316 132 HOH HOH . E 5 HOH A 17 317 142 HOH HOH . E 5 HOH A 18 318 112 HOH HOH . E 5 HOH A 19 319 48 HOH HOH . E 5 HOH A 20 320 131 HOH HOH . E 5 HOH A 21 321 60 HOH HOH . E 5 HOH A 22 322 34 HOH HOH . E 5 HOH A 23 323 114 HOH HOH . E 5 HOH A 24 324 56 HOH HOH . E 5 HOH A 25 325 62 HOH HOH . E 5 HOH A 26 326 108 HOH HOH . E 5 HOH A 27 327 70 HOH HOH . E 5 HOH A 28 328 147 HOH HOH . E 5 HOH A 29 329 125 HOH HOH . E 5 HOH A 30 330 24 HOH HOH . E 5 HOH A 31 331 78 HOH HOH . E 5 HOH A 32 332 103 HOH HOH . E 5 HOH A 33 333 116 HOH HOH . E 5 HOH A 34 334 85 HOH HOH . E 5 HOH A 35 335 137 HOH HOH . E 5 HOH A 36 336 80 HOH HOH . E 5 HOH A 37 337 50 HOH HOH . E 5 HOH A 38 338 55 HOH HOH . E 5 HOH A 39 339 77 HOH HOH . E 5 HOH A 40 340 54 HOH HOH . E 5 HOH A 41 341 144 HOH HOH . E 5 HOH A 42 342 73 HOH HOH . E 5 HOH A 43 343 59 HOH HOH . E 5 HOH A 44 344 84 HOH HOH . E 5 HOH A 45 345 51 HOH HOH . E 5 HOH A 46 346 7 HOH HOH . E 5 HOH A 47 347 88 HOH HOH . E 5 HOH A 48 348 17 HOH HOH . E 5 HOH A 49 349 110 HOH HOH . E 5 HOH A 50 350 1 HOH HOH . E 5 HOH A 51 351 92 HOH HOH . E 5 HOH A 52 352 69 HOH HOH . E 5 HOH A 53 353 21 HOH HOH . E 5 HOH A 54 354 81 HOH HOH . E 5 HOH A 55 355 111 HOH HOH . E 5 HOH A 56 356 124 HOH HOH . E 5 HOH A 57 357 71 HOH HOH . E 5 HOH A 58 358 26 HOH HOH . E 5 HOH A 59 359 83 HOH HOH . E 5 HOH A 60 360 35 HOH HOH . E 5 HOH A 61 361 33 HOH HOH . E 5 HOH A 62 362 14 HOH HOH . E 5 HOH A 63 363 117 HOH HOH . E 5 HOH A 64 364 76 HOH HOH . E 5 HOH A 65 365 91 HOH HOH . E 5 HOH A 66 366 2 HOH HOH . E 5 HOH A 67 367 107 HOH HOH . E 5 HOH A 68 368 94 HOH HOH . E 5 HOH A 69 369 61 HOH HOH . E 5 HOH A 70 370 90 HOH HOH . E 5 HOH A 71 371 72 HOH HOH . E 5 HOH A 72 372 16 HOH HOH . E 5 HOH A 73 373 150 HOH HOH . E 5 HOH A 74 374 46 HOH HOH . E 5 HOH A 75 375 44 HOH HOH . E 5 HOH A 76 376 140 HOH HOH . E 5 HOH A 77 377 39 HOH HOH . E 5 HOH A 78 378 4 HOH HOH . E 5 HOH A 79 379 82 HOH HOH . E 5 HOH A 80 380 87 HOH HOH . E 5 HOH A 81 381 18 HOH HOH . E 5 HOH A 82 382 52 HOH HOH . E 5 HOH A 83 383 6 HOH HOH . E 5 HOH A 84 384 58 HOH HOH . E 5 HOH A 85 385 45 HOH HOH . E 5 HOH A 86 386 10 HOH HOH . E 5 HOH A 87 387 40 HOH HOH . E 5 HOH A 88 388 109 HOH HOH . E 5 HOH A 89 389 119 HOH HOH . E 5 HOH A 90 390 32 HOH HOH . E 5 HOH A 91 391 128 HOH HOH . E 5 HOH A 92 392 20 HOH HOH . E 5 HOH A 93 393 123 HOH HOH . E 5 HOH A 94 394 47 HOH HOH . E 5 HOH A 95 395 97 HOH HOH . E 5 HOH A 96 396 64 HOH HOH . E 5 HOH A 97 397 75 HOH HOH . E 5 HOH A 98 398 96 HOH HOH . E 5 HOH A 99 399 133 HOH HOH . E 5 HOH A 100 400 8 HOH HOH . E 5 HOH A 101 401 113 HOH HOH . E 5 HOH A 102 402 141 HOH HOH . E 5 HOH A 103 403 27 HOH HOH . E 5 HOH A 104 404 57 HOH HOH . E 5 HOH A 105 405 74 HOH HOH . E 5 HOH A 106 406 105 HOH HOH . E 5 HOH A 107 407 30 HOH HOH . E 5 HOH A 108 408 102 HOH HOH . E 5 HOH A 109 409 129 HOH HOH . E 5 HOH A 110 410 11 HOH HOH . E 5 HOH A 111 411 15 HOH HOH . E 5 HOH A 112 412 143 HOH HOH . E 5 HOH A 113 413 126 HOH HOH . E 5 HOH A 114 414 37 HOH HOH . E 5 HOH A 115 415 139 HOH HOH . E 5 HOH A 116 416 31 HOH HOH . E 5 HOH A 117 417 122 HOH HOH . E 5 HOH A 118 418 120 HOH HOH . E 5 HOH A 119 419 118 HOH HOH . E 5 HOH A 120 420 49 HOH HOH . E 5 HOH A 121 421 145 HOH HOH . E 5 HOH A 122 422 42 HOH HOH . E 5 HOH A 123 423 121 HOH HOH . E 5 HOH A 124 424 98 HOH HOH . E 5 HOH A 125 425 36 HOH HOH . E 5 HOH A 126 426 95 HOH HOH . E 5 HOH A 127 427 99 HOH HOH . E 5 HOH A 128 428 19 HOH HOH . E 5 HOH A 129 429 101 HOH HOH . E 5 HOH A 130 430 134 HOH HOH . E 5 HOH A 131 431 115 HOH HOH . E 5 HOH A 132 432 79 HOH HOH . E 5 HOH A 133 433 146 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 -9.899 6.738 17.725 1 15.19 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -9.351 6.354 16.379 1 16.54 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -10.041 5.514 18.603 1 16.69 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -8.997 7.751 18.378 1 19.73 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -11.326 7.408 17.448 1 15.93 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -12.521 7.408 18.521 1 14.88 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -13.237 6.091 18.533 1 11.81 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -12.08 7.893 19.874 1 16.1 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -13.513 8.457 17.819 1 13.11 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -13.12 9.822 17.662 1 17.26 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -14.363 10.683 17.535 1 14.65 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -15.085 10.318 16.363 1 18.24 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -15.315 10.448 18.699 1 21.41 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -15.937 11.695 19.001 1 19.42 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -16.385 9.532 18.165 1 16.24 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -17.634 9.785 18.805 1 15.62 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -16.426 9.926 16.705 1 13.41 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -16.801 8.821 15.806 1 14.89 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -16.185 7.625 15.738 1 13.86 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -16.755 6.861 14.782 1 12.46 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -17.759 7.565 14.222 1 12.24 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -18.757 7.341 13.155 1 14.91 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -18.808 6.256 12.517 1 13.39 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -19.606 8.343 12.874 1 13.6 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -19.582 9.52 13.522 1 18.47 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -20.49 10.461 13.168 1 18.1 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -18.693 9.793 14.51 1 15.89 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -17.774 8.87 14.891 1 15.47 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #