data_4JDI # _model_server_result.job_id 3GwqBxS7rMR8nnebG0yutQ _model_server_result.datetime_utc '2024-11-26 10:12:11' _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 4jdi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1000}' # _entry.id 4JDI # _exptl.entry_id 4JDI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 4JDI _cell.length_a 61.912 _cell.length_b 61.912 _cell.length_c 181.56 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 C _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 C LYS 228 A LYS 473 1_555 A N SEP 229 A SEP 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C SEP 229 A SEP 474 1_555 A N LEU 230 A LEU 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? metalc ? metalc1 A OD2 ASP 213 A ASP 458 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? metalc ? metalc2 A OD1 ASP 213 A ASP 458 1_555 E MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc3 A OD2 ASP 213 A ASP 458 1_555 E MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc4 C O2A ANP . A ANP 1000 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc5 C O1B ANP . A ANP 1000 1_555 E MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc6 D MG MG . A MG 1001 1_555 F O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? metalc ? metalc7 D MG MG . A MG 1001 1_555 F O HOH . A HOH 1123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc8 D MG MG . A MG 1001 1_555 F O HOH . A HOH 1186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc9 E MG MG . A MG 1002 1_555 F O HOH . A HOH 1232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc10 E MG MG . A MG 1002 1_555 F O HOH . A HOH 1233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc11 E MG MG . A MG 1002 1_555 F O HOH . A HOH 1234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 PG O1G ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 4JDI _atom_sites.fract_transf_matrix[1][1] 0.016152 _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] 0.016152 _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] 0.005508 _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 ANP A 1 1000 1000 ANP ANP . D 4 MG A 1 1001 1001 MG MG . E 4 MG A 1 1002 1002 MG MG . F 5 HOH A 1 1101 1 HOH HOH . F 5 HOH A 2 1102 2 HOH HOH . F 5 HOH A 3 1103 3 HOH HOH . F 5 HOH A 4 1104 4 HOH HOH . F 5 HOH A 5 1105 5 HOH HOH . F 5 HOH A 6 1106 6 HOH HOH . F 5 HOH A 7 1107 7 HOH HOH . F 5 HOH A 8 1108 8 HOH HOH . F 5 HOH A 9 1109 9 HOH HOH . F 5 HOH A 10 1110 10 HOH HOH . F 5 HOH A 11 1111 11 HOH HOH . F 5 HOH A 12 1112 12 HOH HOH . F 5 HOH A 13 1113 13 HOH HOH . F 5 HOH A 14 1114 14 HOH HOH . F 5 HOH A 15 1115 15 HOH HOH . F 5 HOH A 16 1116 16 HOH HOH . F 5 HOH A 17 1117 17 HOH HOH . F 5 HOH A 18 1118 18 HOH HOH . F 5 HOH A 19 1119 19 HOH HOH . F 5 HOH A 20 1120 20 HOH HOH . F 5 HOH A 21 1121 21 HOH HOH . F 5 HOH A 22 1122 22 HOH HOH . F 5 HOH A 23 1123 23 HOH HOH . F 5 HOH A 24 1124 24 HOH HOH . F 5 HOH A 25 1125 25 HOH HOH . F 5 HOH A 26 1126 26 HOH HOH . F 5 HOH A 27 1127 27 HOH HOH . F 5 HOH A 28 1128 28 HOH HOH . F 5 HOH A 29 1129 29 HOH HOH . F 5 HOH A 30 1130 30 HOH HOH . F 5 HOH A 31 1131 31 HOH HOH . F 5 HOH A 32 1132 32 HOH HOH . F 5 HOH A 33 1133 33 HOH HOH . F 5 HOH A 34 1134 34 HOH HOH . F 5 HOH A 35 1135 35 HOH HOH . F 5 HOH A 36 1136 36 HOH HOH . F 5 HOH A 37 1137 37 HOH HOH . F 5 HOH A 38 1138 38 HOH HOH . F 5 HOH A 39 1139 39 HOH HOH . F 5 HOH A 40 1140 40 HOH HOH . F 5 HOH A 41 1141 41 HOH HOH . F 5 HOH A 42 1142 42 HOH HOH . F 5 HOH A 43 1143 43 HOH HOH . F 5 HOH A 44 1144 44 HOH HOH . F 5 HOH A 45 1145 45 HOH HOH . F 5 HOH A 46 1146 46 HOH HOH . F 5 HOH A 47 1147 47 HOH HOH . F 5 HOH A 48 1148 48 HOH HOH . F 5 HOH A 49 1149 49 HOH HOH . F 5 HOH A 50 1150 50 HOH HOH . F 5 HOH A 51 1151 51 HOH HOH . F 5 HOH A 52 1152 52 HOH HOH . F 5 HOH A 53 1153 53 HOH HOH . F 5 HOH A 54 1154 54 HOH HOH . F 5 HOH A 55 1155 55 HOH HOH . F 5 HOH A 56 1156 56 HOH HOH . F 5 HOH A 57 1157 57 HOH HOH . F 5 HOH A 58 1158 58 HOH HOH . F 5 HOH A 59 1159 59 HOH HOH . F 5 HOH A 60 1160 60 HOH HOH . F 5 HOH A 61 1161 61 HOH HOH . F 5 HOH A 62 1162 62 HOH HOH . F 5 HOH A 63 1163 63 HOH HOH . F 5 HOH A 64 1164 64 HOH HOH . F 5 HOH A 65 1165 65 HOH HOH . F 5 HOH A 66 1166 66 HOH HOH . F 5 HOH A 67 1167 67 HOH HOH . F 5 HOH A 68 1168 68 HOH HOH . F 5 HOH A 69 1169 69 HOH HOH . F 5 HOH A 70 1170 70 HOH HOH . F 5 HOH A 71 1171 71 HOH HOH . F 5 HOH A 72 1172 72 HOH HOH . F 5 HOH A 73 1173 73 HOH HOH . F 5 HOH A 74 1174 74 HOH HOH . F 5 HOH A 75 1175 75 HOH HOH . F 5 HOH A 76 1176 76 HOH HOH . F 5 HOH A 77 1177 77 HOH HOH . F 5 HOH A 78 1178 78 HOH HOH . F 5 HOH A 79 1179 79 HOH HOH . F 5 HOH A 80 1180 80 HOH HOH . F 5 HOH A 81 1181 81 HOH HOH . F 5 HOH A 82 1182 82 HOH HOH . F 5 HOH A 83 1183 83 HOH HOH . F 5 HOH A 84 1184 84 HOH HOH . F 5 HOH A 85 1185 85 HOH HOH . F 5 HOH A 86 1186 86 HOH HOH . F 5 HOH A 87 1187 87 HOH HOH . F 5 HOH A 88 1188 88 HOH HOH . F 5 HOH A 89 1189 89 HOH HOH . F 5 HOH A 90 1190 90 HOH HOH . F 5 HOH A 91 1191 91 HOH HOH . F 5 HOH A 92 1192 92 HOH HOH . F 5 HOH A 93 1193 93 HOH HOH . F 5 HOH A 94 1194 94 HOH HOH . F 5 HOH A 95 1195 95 HOH HOH . F 5 HOH A 96 1196 96 HOH HOH . F 5 HOH A 97 1197 97 HOH HOH . F 5 HOH A 98 1198 98 HOH HOH . F 5 HOH A 99 1199 99 HOH HOH . F 5 HOH A 100 1200 100 HOH HOH . F 5 HOH A 101 1201 101 HOH HOH . F 5 HOH A 102 1202 102 HOH HOH . F 5 HOH A 103 1203 103 HOH HOH . F 5 HOH A 104 1204 104 HOH HOH . F 5 HOH A 105 1205 105 HOH HOH . F 5 HOH A 106 1206 107 HOH HOH . F 5 HOH A 107 1207 108 HOH HOH . F 5 HOH A 108 1208 109 HOH HOH . F 5 HOH A 109 1209 110 HOH HOH . F 5 HOH A 110 1210 111 HOH HOH . F 5 HOH A 111 1211 112 HOH HOH . F 5 HOH A 112 1212 113 HOH HOH . F 5 HOH A 113 1213 115 HOH HOH . F 5 HOH A 114 1214 116 HOH HOH . F 5 HOH A 115 1215 117 HOH HOH . F 5 HOH A 116 1216 118 HOH HOH . F 5 HOH A 117 1217 119 HOH HOH . F 5 HOH A 118 1218 120 HOH HOH . F 5 HOH A 119 1219 121 HOH HOH . F 5 HOH A 120 1220 124 HOH HOH . F 5 HOH A 121 1221 125 HOH HOH . F 5 HOH A 122 1222 126 HOH HOH . F 5 HOH A 123 1223 127 HOH HOH . F 5 HOH A 124 1224 128 HOH HOH . F 5 HOH A 125 1225 130 HOH HOH . F 5 HOH A 126 1226 131 HOH HOH . F 5 HOH A 127 1227 132 HOH HOH . F 5 HOH A 128 1228 133 HOH HOH . F 5 HOH A 129 1229 134 HOH HOH . F 5 HOH A 130 1230 135 HOH HOH . F 5 HOH A 131 1231 136 HOH HOH . F 5 HOH A 132 1232 137 HOH HOH . F 5 HOH A 133 1233 138 HOH HOH . F 5 HOH A 134 1234 139 HOH HOH . G 5 HOH B 1 101 106 HOH HOH . G 5 HOH B 2 102 114 HOH HOH . G 5 HOH B 3 103 122 HOH HOH . G 5 HOH B 4 104 123 HOH HOH . G 5 HOH B 5 105 129 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 ANP . . . C 3 -22.558 18.893 -12.43 0.8 28.42 ? PB ANP 1000 A 1 HETATM 2 O O1B ANP . . . C 3 -21.207 18.248 -12.375 0.8 27.31 ? O1B ANP 1000 A 1 HETATM 3 O O2B ANP . . . C 3 -22.483 20.181 -13.389 0.8 29.22 ? O2B ANP 1000 A 1 HETATM 4 N N3B ANP . . . C 3 -23.08 19.31 -10.834 0.8 26.58 ? N3B ANP 1000 A 1 HETATM 5 P PA ANP . . . C 3 -24.263 16.582 -12.785 0.8 29.94 ? PA ANP 1000 A 1 HETATM 6 O O1A ANP . . . C 3 -23.443 15.441 -13.372 0.8 27.98 ? O1A ANP 1000 A 1 HETATM 7 O O2A ANP . . . C 3 -24.559 16.608 -11.314 0.8 29.67 ? O2A ANP 1000 A 1 HETATM 8 O O3A ANP . . . C 3 -23.621 17.983 -13.233 0.8 28.41 ? O3A ANP 1000 A 1 HETATM 9 O O5' ANP . . . C 3 -25.646 16.637 -13.594 1 31.58 ? O5' ANP 1000 A 1 HETATM 10 C C5' ANP . . . C 3 -26.706 17.488 -13.143 1 33.48 ? C5' ANP 1000 A 1 HETATM 11 C C4' ANP . . . C 3 -28.002 16.682 -12.995 1 32.64 ? C4' ANP 1000 A 1 HETATM 12 O O4' ANP . . . C 3 -28.443 16.166 -14.259 1 33.16 ? O4' ANP 1000 A 1 HETATM 13 C C3' ANP . . . C 3 -27.838 15.434 -12.141 1 33.13 ? C3' ANP 1000 A 1 HETATM 14 O O3' ANP . . . C 3 -27.875 15.741 -10.736 1 36.91 ? O3' ANP 1000 A 1 HETATM 15 C C2' ANP . . . C 3 -28.92 14.485 -12.64 1 33.22 ? C2' ANP 1000 A 1 HETATM 16 O O2' ANP . . . C 3 -30.219 14.773 -12.107 1 33.76 ? O2' ANP 1000 A 1 HETATM 17 C C1' ANP . . . C 3 -28.947 14.825 -14.119 1 33.17 ? C1' ANP 1000 A 1 HETATM 18 N N9 ANP . . . C 3 -28.056 13.861 -14.83 1 33.14 ? N9 ANP 1000 A 1 HETATM 19 C C8 ANP . . . C 3 -26.708 13.963 -14.966 1 30.48 ? C8 ANP 1000 A 1 HETATM 20 N N7 ANP . . . C 3 -26.21 12.928 -15.681 1 31.81 ? N7 ANP 1000 A 1 HETATM 21 C C5 ANP . . . C 3 -27.246 12.128 -15.995 1 30.89 ? C5 ANP 1000 A 1 HETATM 22 C C6 ANP . . . C 3 -27.398 10.865 -16.745 1 29.6 ? C6 ANP 1000 A 1 HETATM 23 N N6 ANP . . . C 3 -26.31 10.26 -17.28 1 26.6 ? N6 ANP 1000 A 1 HETATM 24 N N1 ANP . . . C 3 -28.654 10.354 -16.856 1 28.59 ? N1 ANP 1000 A 1 HETATM 25 C C2 ANP . . . C 3 -29.734 10.971 -16.32 1 30.31 ? C2 ANP 1000 A 1 HETATM 26 N N3 ANP . . . C 3 -29.664 12.135 -15.633 1 31.95 ? N3 ANP 1000 A 1 HETATM 27 C C4 ANP . . . C 3 -28.463 12.742 -15.437 1 31.93 ? C4 ANP 1000 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #