data_1DOA # _model_server_result.job_id 87Y6_YFIt8rgGDaxSawEhA _model_server_result.datetime_utc '2024-11-04 20:36:57' _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 1doa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":198}' # _entry.id 1DOA # _exptl.entry_id 1DOA _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 120 _cell.entry_id 1DOA _cell.length_a 83.94 _cell.length_b 83.94 _cell.length_c 191.16 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DOA _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 2 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_645 -y+1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 125.91 -72.694172 0 3 'crystal symmetry operation' 3_765 -x+y+2,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 125.91 72.694172 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 covale ? covale1 A SG CMT 191 A CMT 188 1_555 F C1 GER . A GER 952 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? covale ? covale2 A C ARG 190 A ARG 187 1_555 A N CMT 191 A CMT 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A ND1 HIS 3 A HIS 0 1_555 D MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? metalc ? metalc2 A OG1 THR 20 A THR 17 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc3 A O THR 38 A THR 35 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc4 C MG MG . A MG 199 1_555 G O HOH . A HOH 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc5 C MG MG . A MG 199 1_555 E O2B GDP . A GDP 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc6 C MG MG . A MG 199 1_555 G O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? metalc ? metalc7 D MG MG . A MG 200 1_555 G O HOH . A HOH 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.904 ? # _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 ? # _atom_sites.entry_id 1DOA _atom_sites.fract_transf_matrix[1][1] 0.011913 _atom_sites.fract_transf_matrix[1][2] 0.006878 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013756 _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] 0.005231 _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 1 199 199 MG MG2 . D 3 MG A 1 200 200 MG MG2 . E 4 GDP A 1 198 198 GDP GDP . F 5 GER A 1 952 952 GER GER . G 6 HOH A 1 701 701 HOH WAT . G 6 HOH A 2 702 702 HOH WAT . G 6 HOH A 3 703 703 HOH WAT . G 6 HOH A 4 704 704 HOH WAT . G 6 HOH A 5 705 705 HOH WAT . G 6 HOH A 6 706 706 HOH WAT . G 6 HOH A 7 707 707 HOH WAT . G 6 HOH A 8 709 709 HOH WAT . G 6 HOH A 9 710 710 HOH WAT . G 6 HOH A 10 711 711 HOH WAT . G 6 HOH A 11 712 712 HOH WAT . G 6 HOH A 12 713 713 HOH WAT . G 6 HOH A 13 714 714 HOH WAT . G 6 HOH A 14 715 715 HOH WAT . G 6 HOH A 15 716 716 HOH WAT . G 6 HOH A 16 718 718 HOH WAT . G 6 HOH A 17 720 720 HOH WAT . G 6 HOH A 18 721 721 HOH WAT . G 6 HOH A 19 722 722 HOH WAT . G 6 HOH A 20 723 723 HOH WAT . G 6 HOH A 21 724 724 HOH WAT . G 6 HOH A 22 725 725 HOH WAT . G 6 HOH A 23 726 726 HOH WAT . G 6 HOH A 24 728 728 HOH WAT . G 6 HOH A 25 729 729 HOH WAT . G 6 HOH A 26 730 730 HOH WAT . G 6 HOH A 27 731 731 HOH WAT . G 6 HOH A 28 732 732 HOH WAT . G 6 HOH A 29 733 733 HOH WAT . G 6 HOH A 30 734 734 HOH WAT . G 6 HOH A 31 735 735 HOH WAT . G 6 HOH A 32 736 736 HOH WAT . G 6 HOH A 33 737 737 HOH WAT . G 6 HOH A 34 745 745 HOH WAT . G 6 HOH A 35 747 747 HOH WAT . G 6 HOH A 36 748 748 HOH WAT . G 6 HOH A 37 749 749 HOH WAT . H 6 HOH B 1 708 708 HOH WAT . H 6 HOH B 2 717 717 HOH WAT . H 6 HOH B 3 719 719 HOH WAT . H 6 HOH B 4 727 727 HOH WAT . H 6 HOH B 5 738 738 HOH WAT . H 6 HOH B 6 739 739 HOH WAT . H 6 HOH B 7 740 740 HOH WAT . H 6 HOH B 8 741 741 HOH WAT . H 6 HOH B 9 742 742 HOH WAT . H 6 HOH B 10 743 743 HOH WAT . H 6 HOH B 11 744 744 HOH WAT . H 6 HOH B 12 746 746 HOH WAT . H 6 HOH B 13 750 750 HOH WAT . # 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 . . . E 4 60.507 9.947 -5.735 1 54.18 ? PB GDP 198 A 1 HETATM 2 O O1B GDP . . . E 4 60.557 11.019 -4.695 1 39.78 ? O1B GDP 198 A 1 HETATM 3 O O2B GDP . . . E 4 61.51 8.966 -5.76 1 49.73 ? O2B GDP 198 A 1 HETATM 4 O O3B GDP . . . E 4 58.997 9.3 -5.733 1 49.45 ? O3B GDP 198 A 1 HETATM 5 O O3A GDP . . . E 4 60.718 10.702 -7.088 1 57.33 ? O3A GDP 198 A 1 HETATM 6 P PA GDP . . . E 4 61.784 10.451 -8.33 1 64.18 ? PA GDP 198 A 1 HETATM 7 O O1A GDP . . . E 4 63.196 10.63 -7.876 1 65.62 ? O1A GDP 198 A 1 HETATM 8 O O2A GDP . . . E 4 61.441 9.075 -8.882 1 59.14 ? O2A GDP 198 A 1 HETATM 9 O O5' GDP . . . E 4 61.372 11.666 -9.22 1 67.96 ? O5' GDP 198 A 1 HETATM 10 C C5' GDP . . . E 4 60.148 11.705 -10.014 1 72.07 ? C5' GDP 198 A 1 HETATM 11 C C4' GDP . . . E 4 60.29 12.227 -11.384 1 72.87 ? C4' GDP 198 A 1 HETATM 12 O O4' GDP . . . E 4 61.151 13.46 -11.398 1 74.46 ? O4' GDP 198 A 1 HETATM 13 C C3' GDP . . . E 4 61.061 11.292 -12.392 1 72.82 ? C3' GDP 198 A 1 HETATM 14 O O3' GDP . . . E 4 60.358 11.41 -13.677 1 74.07 ? O3' GDP 198 A 1 HETATM 15 C C2' GDP . . . E 4 62.507 11.837 -12.554 1 73.29 ? C2' GDP 198 A 1 HETATM 16 O O2' GDP . . . E 4 63.213 11.595 -13.781 1 71.33 ? O2' GDP 198 A 1 HETATM 17 C C1' GDP . . . E 4 62.332 13.357 -12.316 1 76.25 ? C1' GDP 198 A 1 HETATM 18 N N9 GDP . . . E 4 63.462 14.01 -11.642 1 81.01 ? N9 GDP 198 A 1 HETATM 19 C C8 GDP . . . E 4 63.985 13.396 -10.394 1 81.81 ? C8 GDP 198 A 1 HETATM 20 N N7 GDP . . . E 4 64.966 14.39 -10.227 1 83.48 ? N7 GDP 198 A 1 HETATM 21 C C5 GDP . . . E 4 65.09 15.394 -11.09 1 84.11 ? C5 GDP 198 A 1 HETATM 22 C C6 GDP . . . E 4 65.803 16.564 -11.42 1 85.9 ? C6 GDP 198 A 1 HETATM 23 O O6 GDP . . . E 4 66.796 16.915 -10.578 1 86.45 ? O6 GDP 198 A 1 HETATM 24 N N1 GDP . . . E 4 65.552 17.332 -12.495 1 86.1 ? N1 GDP 198 A 1 HETATM 25 C C2 GDP . . . E 4 64.441 16.909 -13.402 1 86.1 ? C2 GDP 198 A 1 HETATM 26 N N2 GDP . . . E 4 64.357 17.784 -14.387 1 85.19 ? N2 GDP 198 A 1 HETATM 27 N N3 GDP . . . E 4 63.774 15.867 -13.15 1 85.39 ? N3 GDP 198 A 1 HETATM 28 C C4 GDP . . . E 4 64.061 15.14 -12.072 1 83.94 ? C4 GDP 198 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #