data_5W2H # _model_server_result.job_id p5t8jOjmfvCVC8pzLVoVDQ _model_server_result.datetime_utc '2024-11-17 00:50:05' _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 5w2h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":703}' # _entry.id 5W2H # _exptl.entry_id 5W2H _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "ADENOSINE-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 5W2H _cell.length_a 78.015 _cell.length_b 78.015 _cell.length_c 85.915 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W2H _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _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,F,G _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 3 _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 OD2 ASP 226 A ASP 385 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc2 A OD1 ASP 226 A ASP 385 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc3 A OD2 ASP 226 A ASP 385 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc4 B MG MG . A MG 701 1_555 D O2A ADP . A ADP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc5 B MG MG . A MG 701 1_555 D O3B ADP . A ADP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc6 B MG MG . A MG 701 1_555 G O HOH . A HOH 854 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc7 B MG MG . A MG 701 1_555 G O HOH . A HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc8 B MG MG . A MG 701 1_555 G O HOH . A HOH 925 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc9 C MG MG . A MG 702 1_555 D O1B ADP . A ADP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc10 C MG MG . A MG 702 1_555 G O HOH . A HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? metalc ? metalc11 C MG MG . A MG 702 1_555 G O HOH . A HOH 849 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc12 C MG MG . A MG 702 1_555 G O HOH . A HOH 859 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc13 C MG MG . A MG 702 1_555 G O HOH . A HOH 919 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _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 ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 5W2H _atom_sites.fract_transf_matrix[1][1] 0.012818 _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] 0.012818 _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] 0.011639 _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 MG A 1 701 501 MG MG . C 2 MG A 1 702 502 MG MG . D 3 ADP A 1 703 1001 ADP ADP . E 4 I3P A 1 704 1002 I3P I3P . F 5 PO4 A 1 705 601 PO4 PO4 . G 6 HOH A 1 800 157 HOH HOH . G 6 HOH A 2 801 101 HOH HOH . G 6 HOH A 3 802 61 HOH HOH . G 6 HOH A 4 803 155 HOH HOH . G 6 HOH A 5 804 93 HOH HOH . G 6 HOH A 6 805 132 HOH HOH . G 6 HOH A 7 806 116 HOH HOH . G 6 HOH A 8 807 161 HOH HOH . G 6 HOH A 9 808 84 HOH HOH . G 6 HOH A 10 809 108 HOH HOH . G 6 HOH A 11 810 154 HOH HOH . G 6 HOH A 12 811 69 HOH HOH . G 6 HOH A 13 812 45 HOH HOH . G 6 HOH A 14 813 128 HOH HOH . G 6 HOH A 15 814 83 HOH HOH . G 6 HOH A 16 815 37 HOH HOH . G 6 HOH A 17 816 21 HOH HOH . G 6 HOH A 18 817 34 HOH HOH . G 6 HOH A 19 818 6 HOH HOH . G 6 HOH A 20 819 106 HOH HOH . G 6 HOH A 21 820 135 HOH HOH . G 6 HOH A 22 821 149 HOH HOH . G 6 HOH A 23 822 166 HOH HOH . G 6 HOH A 24 823 38 HOH HOH . G 6 HOH A 25 824 126 HOH HOH . G 6 HOH A 26 825 87 HOH HOH . G 6 HOH A 27 826 97 HOH HOH . G 6 HOH A 28 827 68 HOH HOH . G 6 HOH A 29 828 57 HOH HOH . G 6 HOH A 30 829 52 HOH HOH . G 6 HOH A 31 830 35 HOH HOH . G 6 HOH A 32 831 99 HOH HOH . G 6 HOH A 33 832 89 HOH HOH . G 6 HOH A 34 833 112 HOH HOH . G 6 HOH A 35 834 3 HOH HOH . G 6 HOH A 36 835 59 HOH HOH . G 6 HOH A 37 836 56 HOH HOH . G 6 HOH A 38 837 47 HOH HOH . G 6 HOH A 39 838 105 HOH HOH . G 6 HOH A 40 839 121 HOH HOH . G 6 HOH A 41 840 109 HOH HOH . G 6 HOH A 42 841 25 HOH HOH . G 6 HOH A 43 842 94 HOH HOH . G 6 HOH A 44 843 11 HOH HOH . G 6 HOH A 45 844 71 HOH HOH . G 6 HOH A 46 845 24 HOH HOH . G 6 HOH A 47 846 66 HOH HOH . G 6 HOH A 48 847 118 HOH HOH . G 6 HOH A 49 848 55 HOH HOH . G 6 HOH A 50 849 152 HOH HOH . G 6 HOH A 51 850 120 HOH HOH . G 6 HOH A 52 851 23 HOH HOH . G 6 HOH A 53 852 123 HOH HOH . G 6 HOH A 54 853 42 HOH HOH . G 6 HOH A 55 854 88 HOH HOH . G 6 HOH A 56 855 20 HOH HOH . G 6 HOH A 57 856 72 HOH HOH . G 6 HOH A 58 857 78 HOH HOH . G 6 HOH A 59 858 142 HOH HOH . G 6 HOH A 60 859 133 HOH HOH . G 6 HOH A 61 860 16 HOH HOH . G 6 HOH A 62 861 117 HOH HOH . G 6 HOH A 63 862 127 HOH HOH . G 6 HOH A 64 863 27 HOH HOH . G 6 HOH A 65 864 39 HOH HOH . G 6 HOH A 66 865 134 HOH HOH . G 6 HOH A 67 866 31 HOH HOH . G 6 HOH A 68 867 80 HOH HOH . G 6 HOH A 69 868 1 HOH HOH . G 6 HOH A 70 869 168 HOH HOH . G 6 HOH A 71 870 58 HOH HOH . G 6 HOH A 72 871 122 HOH HOH . G 6 HOH A 73 872 18 HOH HOH . G 6 HOH A 74 873 9 HOH HOH . G 6 HOH A 75 874 98 HOH HOH . G 6 HOH A 76 875 51 HOH HOH . G 6 HOH A 77 876 100 HOH HOH . G 6 HOH A 78 877 131 HOH HOH . G 6 HOH A 79 878 141 HOH HOH . G 6 HOH A 80 879 107 HOH HOH . G 6 HOH A 81 880 5 HOH HOH . G 6 HOH A 82 881 4 HOH HOH . G 6 HOH A 83 882 46 HOH HOH . G 6 HOH A 84 883 81 HOH HOH . G 6 HOH A 85 884 12 HOH HOH . G 6 HOH A 86 885 110 HOH HOH . G 6 HOH A 87 886 143 HOH HOH . G 6 HOH A 88 887 145 HOH HOH . G 6 HOH A 89 888 13 HOH HOH . G 6 HOH A 90 889 28 HOH HOH . G 6 HOH A 91 890 2 HOH HOH . G 6 HOH A 92 891 148 HOH HOH . G 6 HOH A 93 892 64 HOH HOH . G 6 HOH A 94 893 70 HOH HOH . G 6 HOH A 95 894 7 HOH HOH . G 6 HOH A 96 895 125 HOH HOH . G 6 HOH A 97 896 76 HOH HOH . G 6 HOH A 98 897 33 HOH HOH . G 6 HOH A 99 898 10 HOH HOH . G 6 HOH A 100 899 41 HOH HOH . G 6 HOH A 101 900 136 HOH HOH . G 6 HOH A 102 901 50 HOH HOH . G 6 HOH A 103 902 44 HOH HOH . G 6 HOH A 104 903 90 HOH HOH . G 6 HOH A 105 904 85 HOH HOH . G 6 HOH A 106 905 96 HOH HOH . G 6 HOH A 107 906 36 HOH HOH . G 6 HOH A 108 907 14 HOH HOH . G 6 HOH A 109 908 137 HOH HOH . G 6 HOH A 110 909 26 HOH HOH . G 6 HOH A 111 910 129 HOH HOH . G 6 HOH A 112 911 17 HOH HOH . G 6 HOH A 113 912 164 HOH HOH . G 6 HOH A 114 913 22 HOH HOH . G 6 HOH A 115 914 8 HOH HOH . G 6 HOH A 116 915 75 HOH HOH . G 6 HOH A 117 916 170 HOH HOH . G 6 HOH A 118 917 32 HOH HOH . G 6 HOH A 119 918 15 HOH HOH . G 6 HOH A 120 919 153 HOH HOH . G 6 HOH A 121 920 49 HOH HOH . G 6 HOH A 122 921 144 HOH HOH . G 6 HOH A 123 922 40 HOH HOH . G 6 HOH A 124 923 159 HOH HOH . G 6 HOH A 125 924 172 HOH HOH . G 6 HOH A 126 925 63 HOH HOH . G 6 HOH A 127 926 60 HOH HOH . G 6 HOH A 128 927 77 HOH HOH . G 6 HOH A 129 928 29 HOH HOH . G 6 HOH A 130 929 95 HOH HOH . G 6 HOH A 131 930 171 HOH HOH . G 6 HOH A 132 931 86 HOH HOH . G 6 HOH A 133 932 43 HOH HOH . G 6 HOH A 134 933 115 HOH HOH . G 6 HOH A 135 934 140 HOH HOH . G 6 HOH A 136 935 19 HOH HOH . G 6 HOH A 137 936 54 HOH HOH . G 6 HOH A 138 937 130 HOH HOH . G 6 HOH A 139 938 67 HOH HOH . G 6 HOH A 140 939 114 HOH HOH . G 6 HOH A 141 940 82 HOH HOH . G 6 HOH A 142 941 102 HOH HOH . G 6 HOH A 143 942 62 HOH HOH . G 6 HOH A 144 943 160 HOH HOH . G 6 HOH A 145 944 30 HOH HOH . G 6 HOH A 146 945 139 HOH HOH . G 6 HOH A 147 946 151 HOH HOH . G 6 HOH A 148 947 124 HOH HOH . G 6 HOH A 149 948 165 HOH HOH . G 6 HOH A 150 949 104 HOH HOH . G 6 HOH A 151 950 91 HOH HOH . G 6 HOH A 152 951 74 HOH HOH . G 6 HOH A 153 952 119 HOH HOH . G 6 HOH A 154 953 53 HOH HOH . G 6 HOH A 155 954 92 HOH HOH . G 6 HOH A 156 955 150 HOH HOH . G 6 HOH A 157 956 167 HOH HOH . G 6 HOH A 158 957 162 HOH HOH . G 6 HOH A 159 958 163 HOH HOH . G 6 HOH A 160 959 48 HOH HOH . G 6 HOH A 161 960 138 HOH HOH . G 6 HOH A 162 961 113 HOH HOH . G 6 HOH A 163 962 158 HOH HOH . G 6 HOH A 164 963 111 HOH HOH . G 6 HOH A 165 964 147 HOH HOH . G 6 HOH A 166 965 169 HOH HOH . G 6 HOH A 167 966 103 HOH HOH . G 6 HOH A 168 967 73 HOH HOH . G 6 HOH A 169 968 65 HOH HOH . G 6 HOH A 170 969 79 HOH HOH . G 6 HOH A 171 970 146 HOH HOH . G 6 HOH A 172 971 156 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 ADP . . . D 3 12.37 21.651 28.553 1 23.78 ? PB ADP 703 A 1 HETATM 2 O O1B ADP . . . D 3 13.247 20.887 27.594 1 28.27 ? O1B ADP 703 A 1 HETATM 3 O O2B ADP . . . D 3 13.104 22.719 29.314 1 26.22 ? O2B ADP 703 A 1 HETATM 4 O O3B ADP . . . D 3 11.471 20.746 29.347 1 20.47 ? O3B ADP 703 A 1 HETATM 5 P PA ADP . . . D 3 10.023 22.43 26.942 1 17.14 ? PA ADP 703 A 1 HETATM 6 O O1A ADP . . . D 3 10.113 22.37 25.453 1 17.46 ? O1A ADP 703 A 1 HETATM 7 O O2A ADP . . . D 3 9.226 21.388 27.686 1 16.91 ? O2A ADP 703 A 1 HETATM 8 O O3A ADP . . . D 3 11.501 22.612 27.557 1 20.12 ? O3A ADP 703 A 1 HETATM 9 O O5' ADP . . . D 3 9.417 23.846 27.319 1 18.39 ? O5' ADP 703 A 1 HETATM 10 C C5' ADP . . . D 3 9.308 24.271 28.673 1 19.15 ? C5' ADP 703 A 1 HETATM 11 C C4' ADP . . . D 3 7.964 24.971 28.901 1 18.53 ? C4' ADP 703 A 1 HETATM 12 O O4' ADP . . . D 3 7.802 26.103 28.028 1 18.17 ? O4' ADP 703 A 1 HETATM 13 C C3' ADP . . . D 3 6.764 24.089 28.649 1 17.71 ? C3' ADP 703 A 1 HETATM 14 O O3' ADP . . . D 3 6.358 23.337 29.798 1 19.92 ? O3' ADP 703 A 1 HETATM 15 C C2' ADP . . . D 3 5.696 25.071 28.239 1 17.22 ? C2' ADP 703 A 1 HETATM 16 O O2' ADP . . . D 3 5.008 25.563 29.383 1 18.83 ? O2' ADP 703 A 1 HETATM 17 C C1' ADP . . . D 3 6.452 26.213 27.592 1 17.56 ? C1' ADP 703 A 1 HETATM 18 N N9 ADP . . . D 3 6.414 26.046 26.122 1 15.71 ? N9 ADP 703 A 1 HETATM 19 C C8 ADP . . . D 3 7.271 25.274 25.406 1 15.28 ? C8 ADP 703 A 1 HETATM 20 N N7 ADP . . . D 3 6.993 25.311 24.092 1 14.53 ? N7 ADP 703 A 1 HETATM 21 C C5 ADP . . . D 3 5.928 26.117 23.956 1 13.35 ? C5 ADP 703 A 1 HETATM 22 C C6 ADP . . . D 3 5.158 26.58 22.805 1 13.49 ? C6 ADP 703 A 1 HETATM 23 N N6 ADP . . . D 3 5.526 26.124 21.571 1 13.95 ? N6 ADP 703 A 1 HETATM 24 N N1 ADP . . . D 3 4.117 27.415 23.044 1 12.57 ? N1 ADP 703 A 1 HETATM 25 C C2 ADP . . . D 3 3.804 27.822 24.296 1 13.15 ? C2 ADP 703 A 1 HETATM 26 N N3 ADP . . . D 3 4.476 27.443 25.395 1 13.81 ? N3 ADP 703 A 1 HETATM 27 C C4 ADP . . . D 3 5.539 26.609 25.282 1 14.36 ? C4 ADP 703 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 27 #