data_1RE0 # _model_server_result.job_id NaggKnEHdnUYdT2zXFv5PA _model_server_result.datetime_utc '2024-10-11 00:31:13' _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 1re0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":700}' # _entry.id 1RE0 # _exptl.entry_id 1RE0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 1RE0 _cell.length_a 64.725 _cell.length_b 72.294 _cell.length_c 119.632 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RE0 _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 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 _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 4 _struct_asym.id D _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 14 A THR 31 1_555 C MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? metalc ? metalc2 D O2B GDP . A GDP 700 1_555 C MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc3 C MG MG . A MG 701 1_555 G O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc4 C MG MG . A MG 701 1_555 G O HOH . A HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc5 C MG MG . A MG 701 1_555 G O HOH . A HOH 742 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc6 C MG MG . A MG 701 1_555 G O HOH . A HOH 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? # _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 148 n n PB O2B GDP sing 149 n n PB O3B GDP sing 150 n n PB O3A GDP sing 151 n n O2B HOB2 GDP sing 152 n n O3B HOB3 GDP sing 153 n n O3A PA GDP sing 154 n n PA O1A GDP doub 155 n n PA O2A GDP sing 156 n n PA O5' GDP sing 157 n n O2A HOA2 GDP sing 158 n n O5' C5' GDP sing 159 n n C5' C4' GDP sing 160 n n C5' H5' GDP sing 161 n n C5' "H5''" GDP sing 162 n n C4' O4' GDP sing 163 n n C4' C3' GDP sing 164 n n C4' H4' GDP sing 165 n n O4' C1' GDP sing 166 n n C3' O3' GDP sing 167 n n C3' C2' GDP sing 168 n n C3' H3' GDP sing 169 n n O3' HO3' GDP sing 170 n n C2' O2' GDP sing 171 n n C2' C1' GDP sing 172 n n C2' H2' GDP sing 173 n n O2' HO2' GDP sing 174 n n C1' N9 GDP sing 175 n n C1' H1' GDP sing 176 n n N9 C8 GDP sing 177 n y N9 C4 GDP sing 178 n y C8 N7 GDP doub 179 n y C8 H8 GDP sing 180 n n N7 C5 GDP sing 181 n y C5 C6 GDP sing 182 n n C5 C4 GDP doub 183 n y C6 O6 GDP doub 184 n n C6 N1 GDP sing 185 n n N1 C2 GDP sing 186 n n N1 HN1 GDP sing 187 n n C2 N2 GDP sing 188 n n C2 N3 GDP doub 189 n n N2 HN21 GDP sing 190 n n N2 HN22 GDP sing 191 n n N3 C4 GDP sing 192 n n # _atom_sites.entry_id 1RE0 _atom_sites.fract_transf_matrix[1][1] 0.01545 _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] 0.013832 _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] 0.008359 _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 3 MG A 1 701 701 MG MG . D 4 GDP A 1 700 700 GDP GDP . E 5 AFB A 1 702 1 AFB BRE . F 6 CIT A 1 703 1 CIT CIT . G 7 HOH A 1 704 1 HOH TIP . G 7 HOH A 2 705 4 HOH TIP . G 7 HOH A 3 706 5 HOH TIP . G 7 HOH A 4 707 8 HOH TIP . G 7 HOH A 5 708 9 HOH TIP . G 7 HOH A 6 709 13 HOH TIP . G 7 HOH A 7 710 14 HOH TIP . G 7 HOH A 8 711 16 HOH TIP . G 7 HOH A 9 712 18 HOH TIP . G 7 HOH A 10 713 19 HOH TIP . G 7 HOH A 11 714 22 HOH TIP . G 7 HOH A 12 715 23 HOH TIP . G 7 HOH A 13 716 24 HOH TIP . G 7 HOH A 14 717 25 HOH TIP . G 7 HOH A 15 718 26 HOH TIP . G 7 HOH A 16 719 27 HOH TIP . G 7 HOH A 17 720 30 HOH TIP . G 7 HOH A 18 721 33 HOH TIP . G 7 HOH A 19 722 37 HOH TIP . G 7 HOH A 20 723 38 HOH TIP . G 7 HOH A 21 724 43 HOH TIP . G 7 HOH A 22 725 44 HOH TIP . G 7 HOH A 23 726 48 HOH TIP . G 7 HOH A 24 727 50 HOH TIP . G 7 HOH A 25 728 55 HOH TIP . G 7 HOH A 26 729 59 HOH TIP . G 7 HOH A 27 730 61 HOH TIP . G 7 HOH A 28 731 62 HOH TIP . G 7 HOH A 29 732 63 HOH TIP . G 7 HOH A 30 733 65 HOH TIP . G 7 HOH A 31 734 66 HOH TIP . G 7 HOH A 32 735 69 HOH TIP . G 7 HOH A 33 736 74 HOH TIP . G 7 HOH A 34 737 76 HOH TIP . G 7 HOH A 35 738 78 HOH TIP . G 7 HOH A 36 739 82 HOH TIP . G 7 HOH A 37 740 83 HOH TIP . G 7 HOH A 38 741 86 HOH TIP . G 7 HOH A 39 742 87 HOH TIP . G 7 HOH A 40 743 88 HOH TIP . G 7 HOH A 41 744 89 HOH TIP . G 7 HOH A 42 745 94 HOH TIP . G 7 HOH A 43 746 100 HOH TIP . G 7 HOH A 44 747 101 HOH TIP . G 7 HOH A 45 748 102 HOH TIP . G 7 HOH A 46 749 109 HOH TIP . G 7 HOH A 47 750 110 HOH TIP . G 7 HOH A 48 751 111 HOH TIP . G 7 HOH A 49 752 113 HOH TIP . H 7 HOH B 1 316 2 HOH TIP . H 7 HOH B 2 317 3 HOH TIP . H 7 HOH B 3 318 6 HOH TIP . H 7 HOH B 4 319 7 HOH TIP . H 7 HOH B 5 320 10 HOH TIP . H 7 HOH B 6 321 11 HOH TIP . H 7 HOH B 7 322 12 HOH TIP . H 7 HOH B 8 323 15 HOH TIP . H 7 HOH B 9 324 17 HOH TIP . H 7 HOH B 10 325 20 HOH TIP . H 7 HOH B 11 326 21 HOH TIP . H 7 HOH B 12 327 28 HOH TIP . H 7 HOH B 13 328 29 HOH TIP . H 7 HOH B 14 329 31 HOH TIP . H 7 HOH B 15 330 32 HOH TIP . H 7 HOH B 16 331 34 HOH TIP . H 7 HOH B 17 332 35 HOH TIP . H 7 HOH B 18 333 36 HOH TIP . H 7 HOH B 19 334 39 HOH TIP . H 7 HOH B 20 335 40 HOH TIP . H 7 HOH B 21 336 41 HOH TIP . H 7 HOH B 22 337 42 HOH TIP . H 7 HOH B 23 338 45 HOH TIP . H 7 HOH B 24 339 46 HOH TIP . H 7 HOH B 25 340 47 HOH TIP . H 7 HOH B 26 341 49 HOH TIP . H 7 HOH B 27 342 51 HOH TIP . H 7 HOH B 28 343 52 HOH TIP . H 7 HOH B 29 344 53 HOH TIP . H 7 HOH B 30 345 54 HOH TIP . H 7 HOH B 31 346 56 HOH TIP . H 7 HOH B 32 347 57 HOH TIP . H 7 HOH B 33 348 58 HOH TIP . H 7 HOH B 34 349 60 HOH TIP . H 7 HOH B 35 350 64 HOH TIP . H 7 HOH B 36 351 67 HOH TIP . H 7 HOH B 37 352 68 HOH TIP . H 7 HOH B 38 353 70 HOH TIP . H 7 HOH B 39 354 71 HOH TIP . H 7 HOH B 40 355 72 HOH TIP . H 7 HOH B 41 356 73 HOH TIP . H 7 HOH B 42 357 75 HOH TIP . H 7 HOH B 43 358 77 HOH TIP . H 7 HOH B 44 359 79 HOH TIP . H 7 HOH B 45 360 80 HOH TIP . H 7 HOH B 46 361 81 HOH TIP . H 7 HOH B 47 362 84 HOH TIP . H 7 HOH B 48 363 85 HOH TIP . H 7 HOH B 49 364 90 HOH TIP . H 7 HOH B 50 365 91 HOH TIP . H 7 HOH B 51 366 92 HOH TIP . H 7 HOH B 52 367 93 HOH TIP . H 7 HOH B 53 368 95 HOH TIP . H 7 HOH B 54 369 96 HOH TIP . H 7 HOH B 55 370 97 HOH TIP . H 7 HOH B 56 371 98 HOH TIP . H 7 HOH B 57 372 99 HOH TIP . H 7 HOH B 58 373 103 HOH TIP . H 7 HOH B 59 374 104 HOH TIP . H 7 HOH B 60 375 105 HOH TIP . H 7 HOH B 61 376 106 HOH TIP . H 7 HOH B 62 377 107 HOH TIP . H 7 HOH B 63 378 108 HOH TIP . H 7 HOH B 64 379 112 HOH TIP . # 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 . . . D 4 27.582 9.435 39.841 1 33.08 ? PB GDP 700 A 1 HETATM 2 O O1B GDP . . . D 4 27.559 8.977 38.438 1 31.21 ? O1B GDP 700 A 1 HETATM 3 O O2B GDP . . . D 4 28.399 8.706 40.817 1 32.34 ? O2B GDP 700 A 1 HETATM 4 O O3B GDP . . . D 4 27.988 10.931 39.844 1 30.19 ? O3B GDP 700 A 1 HETATM 5 O O3A GDP . . . D 4 26.074 9.493 40.44 1 34.17 ? O3A GDP 700 A 1 HETATM 6 P PA GDP . . . D 4 25.491 8.903 41.842 1 38.07 ? PA GDP 700 A 1 HETATM 7 O O1A GDP . . . D 4 25.6 7.419 41.847 1 34.75 ? O1A GDP 700 A 1 HETATM 8 O O2A GDP . . . D 4 26.056 9.684 42.952 1 37.41 ? O2A GDP 700 A 1 HETATM 9 O O5' GDP . . . D 4 23.922 9.293 41.621 1 38.83 ? O5' GDP 700 A 1 HETATM 10 C C5' GDP . . . D 4 23.505 10.676 41.632 1 40.93 ? C5' GDP 700 A 1 HETATM 11 C C4' GDP . . . D 4 22.118 10.82 42.28 1 42.98 ? C4' GDP 700 A 1 HETATM 12 O O4' GDP . . . D 4 21.181 10.047 41.518 1 41.13 ? O4' GDP 700 A 1 HETATM 13 C C3' GDP . . . D 4 22.028 10.29 43.718 1 43.37 ? C3' GDP 700 A 1 HETATM 14 O O3' GDP . . . D 4 21.251 11.179 44.486 1 43.95 ? O3' GDP 700 A 1 HETATM 15 C C2' GDP . . . D 4 21.403 8.904 43.58 1 43.64 ? C2' GDP 700 A 1 HETATM 16 O O2' GDP . . . D 4 20.732 8.355 44.729 1 45.53 ? O2' GDP 700 A 1 HETATM 17 C C1' GDP . . . D 4 20.515 9.097 42.371 1 42.64 ? C1' GDP 700 A 1 HETATM 18 N N9 GDP . . . D 4 20.307 7.852 41.613 1 42.83 ? N9 GDP 700 A 1 HETATM 19 C C8 GDP . . . D 4 21.207 6.927 41.156 1 42.9 ? C8 GDP 700 A 1 HETATM 20 N N7 GDP . . . D 4 20.712 5.922 40.512 1 42.56 ? N7 GDP 700 A 1 HETATM 21 C C5 GDP . . . D 4 19.345 6.181 40.535 1 42.68 ? C5 GDP 700 A 1 HETATM 22 C C6 GDP . . . D 4 18.24 5.424 39.974 1 42.57 ? C6 GDP 700 A 1 HETATM 23 O O6 GDP . . . D 4 18.282 4.36 39.349 1 40.57 ? O6 GDP 700 A 1 HETATM 24 N N1 GDP . . . D 4 16.99 6.044 40.224 1 41.89 ? N1 GDP 700 A 1 HETATM 25 C C2 GDP . . . D 4 16.805 7.24 40.916 1 43.25 ? C2 GDP 700 A 1 HETATM 26 N N2 GDP . . . D 4 15.55 7.667 41.048 1 42.58 ? N2 GDP 700 A 1 HETATM 27 N N3 GDP . . . D 4 17.834 7.957 41.44 1 43.93 ? N3 GDP 700 A 1 HETATM 28 C C4 GDP . . . D 4 19.073 7.368 41.213 1 43.59 ? C4 GDP 700 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 28 #