data_1Z28 # _model_server_result.job_id 6EBqTQfczzOlh_lKqaRlzg _model_server_result.datetime_utc '2024-11-07 04:33:15' _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 1z28 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1001}' # _entry.id 1Z28 # _exptl.entry_id 1Z28 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-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 1Z28 _cell.length_a 72.24 _cell.length_b 122.53 _cell.length_c 43.82 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z28 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 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 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 1Z28 _atom_sites.fract_transf_matrix[1][1] 0.013843 _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] 0.008161 _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] 0.022821 _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 A3P A 1 1001 1 A3P A3P . C 3 HOH A 1 1002 1 HOH WAT . C 3 HOH A 2 1003 2 HOH WAT . C 3 HOH A 3 1004 3 HOH WAT . C 3 HOH A 4 1005 4 HOH WAT . C 3 HOH A 5 1006 5 HOH WAT . C 3 HOH A 6 1007 6 HOH WAT . C 3 HOH A 7 1008 7 HOH WAT . C 3 HOH A 8 1009 8 HOH WAT . C 3 HOH A 9 1010 9 HOH WAT . C 3 HOH A 10 1011 10 HOH WAT . C 3 HOH A 11 1012 11 HOH WAT . C 3 HOH A 12 1013 12 HOH WAT . C 3 HOH A 13 1014 13 HOH WAT . C 3 HOH A 14 1015 14 HOH WAT . C 3 HOH A 15 1016 15 HOH WAT . C 3 HOH A 16 1017 16 HOH WAT . C 3 HOH A 17 1018 17 HOH WAT . C 3 HOH A 18 1019 18 HOH WAT . C 3 HOH A 19 1020 19 HOH WAT . C 3 HOH A 20 1021 20 HOH WAT . C 3 HOH A 21 1022 21 HOH WAT . C 3 HOH A 22 1023 22 HOH WAT . C 3 HOH A 23 1024 23 HOH WAT . C 3 HOH A 24 1025 24 HOH WAT . C 3 HOH A 25 1026 25 HOH WAT . C 3 HOH A 26 1027 26 HOH WAT . C 3 HOH A 27 1028 27 HOH WAT . C 3 HOH A 28 1029 28 HOH WAT . C 3 HOH A 29 1030 29 HOH WAT . C 3 HOH A 30 1031 30 HOH WAT . C 3 HOH A 31 1032 31 HOH WAT . C 3 HOH A 32 1033 32 HOH WAT . C 3 HOH A 33 1034 33 HOH WAT . C 3 HOH A 34 1035 34 HOH WAT . C 3 HOH A 35 1036 35 HOH WAT . C 3 HOH A 36 1037 36 HOH WAT . C 3 HOH A 37 1038 37 HOH WAT . C 3 HOH A 38 1039 38 HOH WAT . C 3 HOH A 39 1040 39 HOH WAT . C 3 HOH A 40 1041 40 HOH WAT . C 3 HOH A 41 1042 41 HOH WAT . C 3 HOH A 42 1043 42 HOH WAT . C 3 HOH A 43 1044 43 HOH WAT . C 3 HOH A 44 1045 44 HOH WAT . C 3 HOH A 45 1046 45 HOH WAT . C 3 HOH A 46 1047 46 HOH WAT . C 3 HOH A 47 1048 47 HOH WAT . C 3 HOH A 48 1049 48 HOH WAT . C 3 HOH A 49 1050 49 HOH WAT . C 3 HOH A 50 1051 50 HOH WAT . C 3 HOH A 51 1052 51 HOH WAT . C 3 HOH A 52 1053 52 HOH WAT . C 3 HOH A 53 1054 53 HOH WAT . C 3 HOH A 54 1055 54 HOH WAT . C 3 HOH A 55 1056 55 HOH WAT . C 3 HOH A 56 1057 56 HOH WAT . C 3 HOH A 57 1058 57 HOH WAT . C 3 HOH A 58 1059 58 HOH WAT . C 3 HOH A 59 1060 59 HOH WAT . C 3 HOH A 60 1061 60 HOH WAT . C 3 HOH A 61 1062 61 HOH WAT . C 3 HOH A 62 1063 62 HOH WAT . C 3 HOH A 63 1064 63 HOH WAT . C 3 HOH A 64 1065 64 HOH WAT . C 3 HOH A 65 1066 65 HOH WAT . C 3 HOH A 66 1067 66 HOH WAT . C 3 HOH A 67 1068 67 HOH WAT . C 3 HOH A 68 1069 68 HOH WAT . C 3 HOH A 69 1070 69 HOH WAT . C 3 HOH A 70 1071 70 HOH WAT . C 3 HOH A 71 1072 71 HOH WAT . C 3 HOH A 72 1073 72 HOH WAT . C 3 HOH A 73 1074 73 HOH WAT . C 3 HOH A 74 1075 74 HOH WAT . C 3 HOH A 75 1076 75 HOH WAT . C 3 HOH A 76 1077 76 HOH WAT . C 3 HOH A 77 1078 77 HOH WAT . C 3 HOH A 78 1079 78 HOH WAT . C 3 HOH A 79 1080 79 HOH WAT . C 3 HOH A 80 1081 80 HOH WAT . C 3 HOH A 81 1082 81 HOH WAT . C 3 HOH A 82 1083 82 HOH WAT . C 3 HOH A 83 1084 83 HOH WAT . C 3 HOH A 84 1085 84 HOH WAT . C 3 HOH A 85 1086 85 HOH WAT . C 3 HOH A 86 1087 86 HOH WAT . C 3 HOH A 87 1088 87 HOH WAT . C 3 HOH A 88 1089 88 HOH WAT . C 3 HOH A 89 1090 89 HOH WAT . C 3 HOH A 90 1091 90 HOH WAT . C 3 HOH A 91 1092 91 HOH WAT . C 3 HOH A 92 1093 92 HOH WAT . C 3 HOH A 93 1094 93 HOH WAT . C 3 HOH A 94 1095 94 HOH WAT . C 3 HOH A 95 1096 95 HOH WAT . C 3 HOH A 96 1097 96 HOH WAT . C 3 HOH A 97 1098 97 HOH WAT . C 3 HOH A 98 1099 98 HOH WAT . C 3 HOH A 99 1100 99 HOH WAT . C 3 HOH A 100 1101 100 HOH WAT . C 3 HOH A 101 1102 101 HOH WAT . C 3 HOH A 102 1103 102 HOH WAT . C 3 HOH A 103 1104 103 HOH WAT . C 3 HOH A 104 1105 104 HOH WAT . C 3 HOH A 105 1106 105 HOH WAT . C 3 HOH A 106 1107 106 HOH WAT . C 3 HOH A 107 1108 107 HOH WAT . C 3 HOH A 108 1109 108 HOH WAT . C 3 HOH A 109 1110 109 HOH WAT . C 3 HOH A 110 1111 110 HOH WAT . C 3 HOH A 111 1112 111 HOH WAT . C 3 HOH A 112 1113 112 HOH WAT . C 3 HOH A 113 1114 113 HOH WAT . C 3 HOH A 114 1115 114 HOH WAT . C 3 HOH A 115 1116 115 HOH WAT . C 3 HOH A 116 1117 116 HOH WAT . C 3 HOH A 117 1118 117 HOH WAT . C 3 HOH A 118 1119 118 HOH WAT . C 3 HOH A 119 1120 119 HOH WAT . C 3 HOH A 120 1121 120 HOH WAT . C 3 HOH A 121 1122 121 HOH WAT . C 3 HOH A 122 1123 122 HOH WAT . C 3 HOH A 123 1124 123 HOH WAT . C 3 HOH A 124 1125 124 HOH WAT . C 3 HOH A 125 1126 125 HOH WAT . C 3 HOH A 126 1127 126 HOH WAT . C 3 HOH A 127 1128 127 HOH WAT . C 3 HOH A 128 1129 128 HOH WAT . C 3 HOH A 129 1130 129 HOH WAT . C 3 HOH A 130 1131 130 HOH WAT . C 3 HOH A 131 1132 131 HOH WAT . C 3 HOH A 132 1133 132 HOH WAT . C 3 HOH A 133 1134 133 HOH WAT . C 3 HOH A 134 1135 134 HOH WAT . C 3 HOH A 135 1136 135 HOH WAT . C 3 HOH A 136 1137 136 HOH WAT . C 3 HOH A 137 1138 137 HOH WAT . C 3 HOH A 138 1139 138 HOH WAT . C 3 HOH A 139 1140 139 HOH WAT . C 3 HOH A 140 1141 140 HOH WAT . C 3 HOH A 141 1142 141 HOH WAT . C 3 HOH A 142 1143 142 HOH WAT . C 3 HOH A 143 1144 143 HOH WAT . C 3 HOH A 144 1145 144 HOH WAT . C 3 HOH A 145 1146 145 HOH WAT . C 3 HOH A 146 1147 146 HOH WAT . C 3 HOH A 147 1148 147 HOH WAT . C 3 HOH A 148 1149 148 HOH WAT . C 3 HOH A 149 1150 149 HOH WAT . C 3 HOH A 150 1151 150 HOH WAT . C 3 HOH A 151 1152 151 HOH WAT . C 3 HOH A 152 1153 152 HOH WAT . C 3 HOH A 153 1154 153 HOH WAT . C 3 HOH A 154 1155 154 HOH WAT . C 3 HOH A 155 1156 155 HOH WAT . C 3 HOH A 156 1157 156 HOH WAT . C 3 HOH A 157 1158 157 HOH WAT . C 3 HOH A 158 1159 158 HOH WAT . C 3 HOH A 159 1160 159 HOH WAT . C 3 HOH A 160 1161 160 HOH WAT . C 3 HOH A 161 1162 161 HOH WAT . C 3 HOH A 162 1163 162 HOH WAT . C 3 HOH A 163 1164 163 HOH WAT . C 3 HOH A 164 1165 164 HOH WAT . C 3 HOH A 165 1166 165 HOH WAT . C 3 HOH A 166 1167 166 HOH WAT . C 3 HOH A 167 1168 167 HOH WAT . C 3 HOH A 168 1169 168 HOH WAT . C 3 HOH A 169 1170 169 HOH WAT . C 3 HOH A 170 1171 170 HOH WAT . C 3 HOH A 171 1172 171 HOH WAT . C 3 HOH A 172 1173 172 HOH WAT . C 3 HOH A 173 1174 173 HOH WAT . C 3 HOH A 174 1175 174 HOH WAT . C 3 HOH A 175 1176 175 HOH WAT . C 3 HOH A 176 1177 176 HOH WAT . C 3 HOH A 177 1178 177 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 P1 A3P . . . B 2 19.956 6.972 18.634 1 10.14 ? P1 A3P 1001 A 1 HETATM 2 O O1P A3P . . . B 2 20.723 6.487 19.797 1 6.33 ? O1P A3P 1001 A 1 HETATM 3 O O2P A3P . . . B 2 20.687 7.61 17.516 1 9.34 ? O2P A3P 1001 A 1 HETATM 4 O O3P A3P . . . B 2 19.085 5.757 18.072 1 8.17 ? O3P A3P 1001 A 1 HETATM 5 P P2 A3P . . . B 2 16.666 13.809 18.656 1 11.37 ? P2 A3P 1001 A 1 HETATM 6 O O4P A3P . . . B 2 15.285 13.533 18.198 1 9.77 ? O4P A3P 1001 A 1 HETATM 7 O O5P A3P . . . B 2 16.875 14.856 19.675 1 10.34 ? O5P A3P 1001 A 1 HETATM 8 O O6P A3P . . . B 2 17.589 14.182 17.388 1 13.69 ? O6P A3P 1001 A 1 HETATM 9 O O5' A3P . . . B 2 17.316 12.454 19.188 1 13.1 ? O5' A3P 1001 A 1 HETATM 10 C C5' A3P . . . B 2 17.47 11.326 18.33 1 10.71 ? C5' A3P 1001 A 1 HETATM 11 C C4' A3P . . . B 2 17.706 10.091 19.188 1 10.52 ? C4' A3P 1001 A 1 HETATM 12 O O4' A3P . . . B 2 16.427 9.773 19.855 1 10.32 ? O4' A3P 1001 A 1 HETATM 13 C C3' A3P . . . B 2 18.055 8.851 18.358 1 9.59 ? C3' A3P 1001 A 1 HETATM 14 O O3' A3P . . . B 2 18.84 7.995 19.203 1 9.15 ? O3' A3P 1001 A 1 HETATM 15 C C2' A3P . . . B 2 16.704 8.223 18.12 1 9.63 ? C2' A3P 1001 A 1 HETATM 16 O O2' A3P . . . B 2 16.853 6.83 17.853 1 11.39 ? O2' A3P 1001 A 1 HETATM 17 C C1' A3P . . . B 2 16.054 8.421 19.473 1 9.5 ? C1' A3P 1001 A 1 HETATM 18 N N9 A3P . . . B 2 14.582 8.196 19.509 1 11.74 ? N9 A3P 1001 A 1 HETATM 19 C C8 A3P . . . B 2 13.653 8.749 18.71 1 9.25 ? C8 A3P 1001 A 1 HETATM 20 N N7 A3P . . . B 2 12.443 8.311 19.081 1 9.05 ? N7 A3P 1001 A 1 HETATM 21 C C5 A3P . . . B 2 12.607 7.482 20.107 1 11.14 ? C5 A3P 1001 A 1 HETATM 22 C C6 A3P . . . B 2 11.738 6.723 20.891 1 9.74 ? C6 A3P 1001 A 1 HETATM 23 N N6 A3P . . . B 2 10.427 6.762 20.678 1 7.24 ? N6 A3P 1001 A 1 HETATM 24 N N1 A3P . . . B 2 12.243 5.947 21.88 1 12.83 ? N1 A3P 1001 A 1 HETATM 25 C C2 A3P . . . B 2 13.559 5.898 22.119 1 11.15 ? C2 A3P 1001 A 1 HETATM 26 N N3 A3P . . . B 2 14.408 6.618 21.381 1 10.3 ? N3 A3P 1001 A 1 HETATM 27 C C4 A3P . . . B 2 13.96 7.409 20.378 1 11.32 ? C4 A3P 1001 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 213 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #