data_3CX6 # _model_server_result.job_id meG5OjCHPqQENFkEFWY4xA _model_server_result.datetime_utc '2024-12-13 03:35:48' _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 3cx6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":775}' # _entry.id 3CX6 # _exptl.entry_id 3CX6 _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 3CX6 _cell.length_a 58.036 _cell.length_b 66.872 _cell.length_c 150.902 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CX6 _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 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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 3CX6 _atom_sites.fract_transf_matrix[1][1] 0.017231 _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] 0.014954 _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] 0.006627 _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 1 675 675 MG MG . D 4 GDP A 1 775 775 GDP GDP . E 5 HOH A 1 776 1 HOH HOH . E 5 HOH A 2 777 2 HOH HOH . E 5 HOH A 3 778 3 HOH HOH . E 5 HOH A 4 779 4 HOH HOH . E 5 HOH A 5 780 5 HOH HOH . E 5 HOH A 6 781 6 HOH HOH . E 5 HOH A 7 782 7 HOH HOH . E 5 HOH A 8 783 8 HOH HOH . E 5 HOH A 9 784 10 HOH HOH . E 5 HOH A 10 785 11 HOH HOH . E 5 HOH A 11 786 12 HOH HOH . E 5 HOH A 12 787 13 HOH HOH . E 5 HOH A 13 788 14 HOH HOH . E 5 HOH A 14 789 15 HOH HOH . E 5 HOH A 15 790 16 HOH HOH . E 5 HOH A 16 791 17 HOH HOH . E 5 HOH A 17 792 18 HOH HOH . E 5 HOH A 18 793 20 HOH HOH . E 5 HOH A 19 794 21 HOH HOH . E 5 HOH A 20 795 22 HOH HOH . E 5 HOH A 21 796 23 HOH HOH . E 5 HOH A 22 797 24 HOH HOH . E 5 HOH A 23 798 25 HOH HOH . E 5 HOH A 24 799 26 HOH HOH . E 5 HOH A 25 800 27 HOH HOH . E 5 HOH A 26 801 28 HOH HOH . E 5 HOH A 27 802 29 HOH HOH . E 5 HOH A 28 803 30 HOH HOH . E 5 HOH A 29 804 32 HOH HOH . E 5 HOH A 30 805 33 HOH HOH . E 5 HOH A 31 806 34 HOH HOH . E 5 HOH A 32 807 38 HOH HOH . E 5 HOH A 33 808 39 HOH HOH . E 5 HOH A 34 809 40 HOH HOH . E 5 HOH A 35 810 41 HOH HOH . E 5 HOH A 36 811 42 HOH HOH . E 5 HOH A 37 812 43 HOH HOH . E 5 HOH A 38 813 44 HOH HOH . E 5 HOH A 39 814 45 HOH HOH . E 5 HOH A 40 815 46 HOH HOH . E 5 HOH A 41 816 49 HOH HOH . E 5 HOH A 42 817 50 HOH HOH . E 5 HOH A 43 818 51 HOH HOH . E 5 HOH A 44 819 52 HOH HOH . E 5 HOH A 45 820 53 HOH HOH . E 5 HOH A 46 821 55 HOH HOH . E 5 HOH A 47 822 56 HOH HOH . E 5 HOH A 48 823 57 HOH HOH . E 5 HOH A 49 824 58 HOH HOH . E 5 HOH A 50 825 59 HOH HOH . E 5 HOH A 51 826 61 HOH HOH . E 5 HOH A 52 827 63 HOH HOH . E 5 HOH A 53 828 64 HOH HOH . E 5 HOH A 54 829 65 HOH HOH . E 5 HOH A 55 830 68 HOH HOH . E 5 HOH A 56 831 69 HOH HOH . E 5 HOH A 57 832 70 HOH HOH . E 5 HOH A 58 833 71 HOH HOH . E 5 HOH A 59 834 72 HOH HOH . E 5 HOH A 60 835 73 HOH HOH . E 5 HOH A 61 836 75 HOH HOH . E 5 HOH A 62 837 76 HOH HOH . E 5 HOH A 63 838 77 HOH HOH . E 5 HOH A 64 839 78 HOH HOH . E 5 HOH A 65 840 79 HOH HOH . E 5 HOH A 66 841 82 HOH HOH . E 5 HOH A 67 842 83 HOH HOH . E 5 HOH A 68 843 85 HOH HOH . E 5 HOH A 69 844 86 HOH HOH . E 5 HOH A 70 845 87 HOH HOH . E 5 HOH A 71 846 88 HOH HOH . E 5 HOH A 72 847 89 HOH HOH . E 5 HOH A 73 848 90 HOH HOH . E 5 HOH A 74 849 93 HOH HOH . E 5 HOH A 75 850 96 HOH HOH . E 5 HOH A 76 851 97 HOH HOH . E 5 HOH A 77 852 98 HOH HOH . E 5 HOH A 78 853 99 HOH HOH . E 5 HOH A 79 854 100 HOH HOH . E 5 HOH A 80 855 101 HOH HOH . E 5 HOH A 81 856 103 HOH HOH . E 5 HOH A 82 857 104 HOH HOH . E 5 HOH A 83 858 105 HOH HOH . E 5 HOH A 84 859 108 HOH HOH . E 5 HOH A 85 860 109 HOH HOH . E 5 HOH A 86 861 111 HOH HOH . E 5 HOH A 87 862 112 HOH HOH . E 5 HOH A 88 863 113 HOH HOH . E 5 HOH A 89 864 114 HOH HOH . E 5 HOH A 90 865 115 HOH HOH . E 5 HOH A 91 866 116 HOH HOH . E 5 HOH A 92 867 117 HOH HOH . E 5 HOH A 93 868 118 HOH HOH . E 5 HOH A 94 869 119 HOH HOH . E 5 HOH A 95 870 120 HOH HOH . E 5 HOH A 96 871 121 HOH HOH . E 5 HOH A 97 872 122 HOH HOH . E 5 HOH A 98 873 124 HOH HOH . E 5 HOH A 99 874 125 HOH HOH . E 5 HOH A 100 875 127 HOH HOH . E 5 HOH A 101 876 128 HOH HOH . E 5 HOH A 102 877 129 HOH HOH . E 5 HOH A 103 878 130 HOH HOH . E 5 HOH A 104 879 131 HOH HOH . E 5 HOH A 105 880 132 HOH HOH . E 5 HOH A 106 881 133 HOH HOH . E 5 HOH A 107 882 134 HOH HOH . E 5 HOH A 108 883 138 HOH HOH . E 5 HOH A 109 884 139 HOH HOH . E 5 HOH A 110 885 140 HOH HOH . E 5 HOH A 111 886 141 HOH HOH . E 5 HOH A 112 887 142 HOH HOH . E 5 HOH A 113 888 143 HOH HOH . E 5 HOH A 114 889 144 HOH HOH . F 5 HOH B 1 9 9 HOH HOH . F 5 HOH B 2 19 19 HOH HOH . F 5 HOH B 3 31 31 HOH HOH . F 5 HOH B 4 35 35 HOH HOH . F 5 HOH B 5 36 36 HOH HOH . F 5 HOH B 6 37 37 HOH HOH . F 5 HOH B 7 47 47 HOH HOH . F 5 HOH B 8 48 48 HOH HOH . F 5 HOH B 9 54 54 HOH HOH . F 5 HOH B 10 60 60 HOH HOH . F 5 HOH B 11 62 62 HOH HOH . F 5 HOH B 12 66 66 HOH HOH . F 5 HOH B 13 67 67 HOH HOH . F 5 HOH B 14 74 74 HOH HOH . F 5 HOH B 15 80 80 HOH HOH . F 5 HOH B 16 81 81 HOH HOH . F 5 HOH B 17 84 84 HOH HOH . F 5 HOH B 18 91 91 HOH HOH . F 5 HOH B 19 92 92 HOH HOH . F 5 HOH B 20 94 94 HOH HOH . F 5 HOH B 21 95 95 HOH HOH . F 5 HOH B 22 102 102 HOH HOH . F 5 HOH B 23 106 106 HOH HOH . F 5 HOH B 24 107 107 HOH HOH . F 5 HOH B 25 110 110 HOH HOH . F 5 HOH B 26 123 123 HOH HOH . F 5 HOH B 27 126 126 HOH HOH . F 5 HOH B 28 135 135 HOH HOH . F 5 HOH B 29 136 136 HOH HOH . F 5 HOH B 30 137 137 HOH HOH . F 5 HOH B 31 145 145 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 . . . D 4 -11.592 -8.76 15.926 1 26.54 ? PB GDP 775 A 1 HETATM 2 O O1B GDP . . . D 4 -13.005 -8.703 15.434 1 25.97 ? O1B GDP 775 A 1 HETATM 3 O O2B GDP . . . D 4 -10.686 -7.964 15.025 1 25.22 ? O2B GDP 775 A 1 HETATM 4 O O3B GDP . . . D 4 -11.502 -8.315 17.371 1 28.4 ? O3B GDP 775 A 1 HETATM 5 O O3A GDP . . . D 4 -11.21 -10.306 15.9 1 28.8 ? O3A GDP 775 A 1 HETATM 6 P PA GDP . . . D 4 -9.743 -10.737 15.468 1 28.77 ? PA GDP 775 A 1 HETATM 7 O O1A GDP . . . D 4 -9.548 -10.634 13.977 1 25.76 ? O1A GDP 775 A 1 HETATM 8 O O2A GDP . . . D 4 -8.694 -10.03 16.227 1 24.72 ? O2A GDP 775 A 1 HETATM 9 O O5' GDP . . . D 4 -9.735 -12.281 15.921 1 29.67 ? O5' GDP 775 A 1 HETATM 10 C C5' GDP . . . D 4 -9.825 -12.737 17.277 1 24.88 ? C5' GDP 775 A 1 HETATM 11 C C4' GDP . . . D 4 -9.023 -14.04 17.304 1 29.85 ? C4' GDP 775 A 1 HETATM 12 O O4' GDP . . . D 4 -9.67 -15.067 16.541 1 30.87 ? O4' GDP 775 A 1 HETATM 13 C C3' GDP . . . D 4 -7.656 -13.894 16.618 1 31.36 ? C3' GDP 775 A 1 HETATM 14 O O3' GDP . . . D 4 -6.729 -14.716 17.297 1 30.46 ? O3' GDP 775 A 1 HETATM 15 C C2' GDP . . . D 4 -7.849 -14.462 15.221 1 32.48 ? C2' GDP 775 A 1 HETATM 16 O O2' GDP . . . D 4 -6.658 -14.967 14.628 1 34.1 ? O2' GDP 775 A 1 HETATM 17 C C1' GDP . . . D 4 -8.807 -15.581 15.505 1 33.04 ? C1' GDP 775 A 1 HETATM 18 N N9 GDP . . . D 4 -9.733 -15.916 14.399 1 35.32 ? N9 GDP 775 A 1 HETATM 19 C C8 GDP . . . D 4 -10.435 -15.083 13.589 1 34.35 ? C8 GDP 775 A 1 HETATM 20 N N7 GDP . . . D 4 -11.218 -15.766 12.716 1 32.5 ? N7 GDP 775 A 1 HETATM 21 C C5 GDP . . . D 4 -11.03 -17.081 12.983 1 35.52 ? C5 GDP 775 A 1 HETATM 22 C C6 GDP . . . D 4 -11.525 -18.394 12.467 1 34.34 ? C6 GDP 775 A 1 HETATM 23 O O6 GDP . . . D 4 -12.363 -18.524 11.549 1 34.92 ? O6 GDP 775 A 1 HETATM 24 N N1 GDP . . . D 4 -11.059 -19.485 13.038 1 34.19 ? N1 GDP 775 A 1 HETATM 25 C C2 GDP . . . D 4 -10.158 -19.52 14.025 1 33.93 ? C2 GDP 775 A 1 HETATM 26 N N2 GDP . . . D 4 -9.774 -20.74 14.479 1 34.6 ? N2 GDP 775 A 1 HETATM 27 N N3 GDP . . . D 4 -9.646 -18.388 14.564 1 35.25 ? N3 GDP 775 A 1 HETATM 28 C C4 GDP . . . D 4 -10.058 -17.169 14.096 1 35.87 ? C4 GDP 775 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #