data_1DAR # _model_server_result.job_id yPKG52MHAh8OksRhBFhpUw _model_server_result.datetime_utc '2025-07-02 00:21:18' _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 1dar # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":692}' # _entry.id 1DAR # _exptl.entry_id 1DAR _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 1DAR _cell.length_a 76.3 _cell.length_b 106.4 _cell.length_c 115.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DAR _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _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 1DAR _atom_sites.fract_transf_matrix[1][1] 0.013106 _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] 0.009398 _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] 0.008651 _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 1 692 406 GDP GDP . C 3 HOH A 1 693 1 HOH HOH . C 3 HOH A 2 694 2 HOH HOH . C 3 HOH A 3 695 3 HOH HOH . C 3 HOH A 4 696 4 HOH HOH . C 3 HOH A 5 697 5 HOH HOH . C 3 HOH A 6 698 6 HOH HOH . C 3 HOH A 7 699 7 HOH HOH . C 3 HOH A 8 700 8 HOH HOH . C 3 HOH A 9 701 9 HOH HOH . C 3 HOH A 10 702 10 HOH HOH . C 3 HOH A 11 703 11 HOH HOH . C 3 HOH A 12 704 12 HOH HOH . C 3 HOH A 13 705 13 HOH HOH . C 3 HOH A 14 706 15 HOH HOH . C 3 HOH A 15 707 16 HOH HOH . C 3 HOH A 16 708 17 HOH HOH . C 3 HOH A 17 709 18 HOH HOH . C 3 HOH A 18 710 19 HOH HOH . C 3 HOH A 19 711 20 HOH HOH . C 3 HOH A 20 712 21 HOH HOH . C 3 HOH A 21 713 22 HOH HOH . C 3 HOH A 22 714 23 HOH HOH . C 3 HOH A 23 715 24 HOH HOH . C 3 HOH A 24 716 25 HOH HOH . C 3 HOH A 25 717 26 HOH HOH . C 3 HOH A 26 718 27 HOH HOH . C 3 HOH A 27 719 28 HOH HOH . C 3 HOH A 28 720 29 HOH HOH . C 3 HOH A 29 721 30 HOH HOH . C 3 HOH A 30 722 31 HOH HOH . C 3 HOH A 31 723 32 HOH HOH . C 3 HOH A 32 724 33 HOH HOH . C 3 HOH A 33 725 34 HOH HOH . C 3 HOH A 34 726 35 HOH HOH . C 3 HOH A 35 727 36 HOH HOH . C 3 HOH A 36 728 38 HOH HOH . C 3 HOH A 37 729 39 HOH HOH . C 3 HOH A 38 730 40 HOH HOH . C 3 HOH A 39 731 41 HOH HOH . C 3 HOH A 40 732 42 HOH HOH . C 3 HOH A 41 733 43 HOH HOH . C 3 HOH A 42 734 44 HOH HOH . C 3 HOH A 43 735 45 HOH HOH . C 3 HOH A 44 736 46 HOH HOH . C 3 HOH A 45 737 47 HOH HOH . C 3 HOH A 46 738 48 HOH HOH . C 3 HOH A 47 739 49 HOH HOH . C 3 HOH A 48 740 50 HOH HOH . C 3 HOH A 49 741 51 HOH HOH . C 3 HOH A 50 742 52 HOH HOH . C 3 HOH A 51 743 53 HOH HOH . C 3 HOH A 52 744 54 HOH HOH . C 3 HOH A 53 745 55 HOH HOH . C 3 HOH A 54 746 56 HOH HOH . C 3 HOH A 55 747 57 HOH HOH . C 3 HOH A 56 748 58 HOH HOH . C 3 HOH A 57 749 59 HOH HOH . C 3 HOH A 58 750 61 HOH HOH . C 3 HOH A 59 751 62 HOH HOH . C 3 HOH A 60 752 63 HOH HOH . C 3 HOH A 61 753 64 HOH HOH . C 3 HOH A 62 754 66 HOH HOH . C 3 HOH A 63 755 67 HOH HOH . C 3 HOH A 64 756 68 HOH HOH . C 3 HOH A 65 757 69 HOH HOH . C 3 HOH A 66 758 70 HOH HOH . C 3 HOH A 67 759 71 HOH HOH . C 3 HOH A 68 760 72 HOH HOH . C 3 HOH A 69 761 73 HOH HOH . C 3 HOH A 70 762 74 HOH HOH . C 3 HOH A 71 763 75 HOH HOH . C 3 HOH A 72 764 76 HOH HOH . C 3 HOH A 73 765 77 HOH HOH . C 3 HOH A 74 766 78 HOH HOH . C 3 HOH A 75 767 79 HOH HOH . C 3 HOH A 76 768 80 HOH HOH . C 3 HOH A 77 769 81 HOH HOH . C 3 HOH A 78 770 82 HOH HOH . C 3 HOH A 79 771 83 HOH HOH . C 3 HOH A 80 772 84 HOH HOH . C 3 HOH A 81 773 85 HOH HOH . C 3 HOH A 82 774 86 HOH HOH . C 3 HOH A 83 775 87 HOH HOH . C 3 HOH A 84 776 88 HOH HOH . C 3 HOH A 85 777 89 HOH HOH . C 3 HOH A 86 778 90 HOH HOH . C 3 HOH A 87 779 91 HOH HOH . C 3 HOH A 88 780 92 HOH HOH . C 3 HOH A 89 781 93 HOH HOH . C 3 HOH A 90 782 94 HOH HOH . C 3 HOH A 91 783 95 HOH HOH . C 3 HOH A 92 784 96 HOH HOH . C 3 HOH A 93 785 97 HOH HOH . C 3 HOH A 94 786 98 HOH HOH . C 3 HOH A 95 787 99 HOH HOH . C 3 HOH A 96 788 100 HOH HOH . C 3 HOH A 97 789 101 HOH HOH . C 3 HOH A 98 790 102 HOH HOH . C 3 HOH A 99 791 103 HOH HOH . C 3 HOH A 100 792 104 HOH HOH . C 3 HOH A 101 793 105 HOH HOH . C 3 HOH A 102 794 106 HOH HOH . C 3 HOH A 103 795 107 HOH HOH . C 3 HOH A 104 796 108 HOH HOH . C 3 HOH A 105 797 109 HOH HOH . C 3 HOH A 106 798 110 HOH HOH . C 3 HOH A 107 799 111 HOH HOH . C 3 HOH A 108 800 112 HOH HOH . C 3 HOH A 109 801 113 HOH HOH . C 3 HOH A 110 802 114 HOH HOH . C 3 HOH A 111 803 115 HOH HOH . C 3 HOH A 112 804 116 HOH HOH . C 3 HOH A 113 805 117 HOH HOH . C 3 HOH A 114 806 118 HOH HOH . C 3 HOH A 115 807 120 HOH HOH . C 3 HOH A 116 808 121 HOH HOH . C 3 HOH A 117 809 122 HOH HOH . C 3 HOH A 118 810 123 HOH HOH . C 3 HOH A 119 811 124 HOH HOH . C 3 HOH A 120 812 125 HOH HOH . C 3 HOH A 121 813 126 HOH HOH . C 3 HOH A 122 814 127 HOH HOH . C 3 HOH A 123 815 128 HOH HOH . C 3 HOH A 124 816 129 HOH HOH . C 3 HOH A 125 817 130 HOH HOH . C 3 HOH A 126 818 131 HOH HOH . C 3 HOH A 127 819 132 HOH HOH . C 3 HOH A 128 820 133 HOH HOH . C 3 HOH A 129 821 134 HOH HOH . C 3 HOH A 130 822 135 HOH HOH . C 3 HOH A 131 823 136 HOH HOH . C 3 HOH A 132 824 137 HOH HOH . C 3 HOH A 133 825 138 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 35.741 31.495 -20.332 1 49.58 ? PB GDP 692 A 1 HETATM 2 O O1B GDP . . . B 2 35.356 30.941 -19.081 1 55.85 ? O1B GDP 692 A 1 HETATM 3 O O2B GDP . . . B 2 34.909 32.86 -20.224 1 44.69 ? O2B GDP 692 A 1 HETATM 4 O O3B GDP . . . B 2 37.268 32.121 -20.226 1 54.89 ? O3B GDP 692 A 1 HETATM 5 O O3A GDP . . . B 2 35.7 30.21 -21.135 1 43.69 ? O3A GDP 692 A 1 HETATM 6 P PA GDP . . . B 2 34.825 29 -20.748 1 42.63 ? PA GDP 692 A 1 HETATM 7 O O1A GDP . . . B 2 35.109 27.855 -21.628 1 47.53 ? O1A GDP 692 A 1 HETATM 8 O O2A GDP . . . B 2 33.341 29.468 -21.13 1 41.37 ? O2A GDP 692 A 1 HETATM 9 O O5' GDP . . . B 2 35.024 28.433 -19.346 1 44.25 ? O5' GDP 692 A 1 HETATM 10 C C5' GDP . . . B 2 36.223 27.748 -19.02 1 45.9 ? C5' GDP 692 A 1 HETATM 11 C C4' GDP . . . B 2 36.001 26.354 -18.391 1 50.14 ? C4' GDP 692 A 1 HETATM 12 O O4' GDP . . . B 2 34.846 26.425 -17.492 1 54.09 ? O4' GDP 692 A 1 HETATM 13 C C3' GDP . . . B 2 35.563 25.244 -19.354 1 49.8 ? C3' GDP 692 A 1 HETATM 14 O O3' GDP . . . B 2 36.129 24.006 -18.952 1 56.55 ? O3' GDP 692 A 1 HETATM 15 C C2' GDP . . . B 2 34.086 25.051 -19.228 1 48.92 ? C2' GDP 692 A 1 HETATM 16 O O2' GDP . . . B 2 33.903 23.698 -19.755 1 43.12 ? O2' GDP 692 A 1 HETATM 17 C C1' GDP . . . B 2 33.887 25.317 -17.685 1 48.57 ? C1' GDP 692 A 1 HETATM 18 N N9 GDP . . . B 2 32.485 25.779 -17.358 1 42.66 ? N9 GDP 692 A 1 HETATM 19 C C8 GDP . . . B 2 31.745 26.844 -17.809 1 40.5 ? C8 GDP 692 A 1 HETATM 20 N N7 GDP . . . B 2 30.516 26.887 -17.413 1 37.34 ? N7 GDP 692 A 1 HETATM 21 C C5 GDP . . . B 2 30.476 25.744 -16.633 1 42.39 ? C5 GDP 692 A 1 HETATM 22 C C6 GDP . . . B 2 29.418 25.22 -15.895 1 44.65 ? C6 GDP 692 A 1 HETATM 23 O O6 GDP . . . B 2 28.243 25.591 -15.834 1 47.71 ? O6 GDP 692 A 1 HETATM 24 N N1 GDP . . . B 2 29.805 24.125 -15.231 1 45 ? N1 GDP 692 A 1 HETATM 25 C C2 GDP . . . B 2 31.03 23.581 -15.249 1 45.47 ? C2 GDP 692 A 1 HETATM 26 N N2 GDP . . . B 2 31.211 22.537 -14.446 1 48.29 ? N2 GDP 692 A 1 HETATM 27 N N3 GDP . . . B 2 32.03 24.036 -15.943 1 43.42 ? N3 GDP 692 A 1 HETATM 28 C C4 GDP . . . B 2 31.665 25.107 -16.599 1 41.23 ? C4 GDP 692 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #