data_5ZJY # _model_server_result.job_id Ewz7r4Dgid-nhWRSNXhEIw _model_server_result.datetime_utc '2024-11-19 17:27:59' _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 5zjy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 5ZJY # _exptl.entry_id 5ZJY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 538.215 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "7-METHYL-GUANOSINE-5'-TRIPHOSPHATE" _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 120 _cell.entry_id 5ZJY _cell.length_a 39.8 _cell.length_b 39.8 _cell.length_c 110.23 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZJY _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31' # _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 _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 B C ACE 1 B ACE 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale2 B C ARG 7 B ARG 7 1_555 B N 2JN 8 B 2JN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale3 B C 2JN 8 B 2JN 8 1_555 B N GLN 9 B GLN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? covale ? covale4 B C LEU 11 B LEU 11 1_555 B N 2JN 12 B 2JN 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? covale ? covale5 B C 2JN 12 B 2JN 12 1_555 B N PHE 13 B PHE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.28 ? covale ? covale6 B C PHE 13 B PHE 13 1_555 B N NH2 14 B NH2 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? # _chem_comp.formula 'C11 H19 N5 O14 P3 1' _chem_comp.formula_weight 538.215 _chem_comp.id MGP _chem_comp.mon_nstd_flag . _chem_comp.name "7-METHYL-GUANOSINE-5'-TRIPHOSPHATE" _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 PA O1A MGP sing 267 n n PA O2A MGP doub 268 n n PA O3A MGP sing 269 n n PA O5' MGP sing 270 n n O3A PB MGP sing 271 n n O5' C5' MGP sing 272 n n PB O1B MGP sing 273 n n PB O2B MGP doub 274 n n PB O3B MGP sing 275 n n O3B PC MGP sing 276 n n PC O1C MGP sing 277 n n PC O2C MGP doub 278 n n PC O3C MGP sing 279 n n C5' C4' MGP sing 280 n n C5' H5' MGP sing 281 n n C5' "H5'A" MGP sing 282 n n C4' O4' MGP sing 283 n n C4' C3' MGP sing 284 n n C4' H4' MGP sing 285 n n O4' C1' MGP sing 286 n n C3' O3' MGP sing 287 n n C3' C2' MGP sing 288 n n C3' H3' MGP sing 289 n n O3' HO3' MGP sing 290 n n C2' O2' MGP sing 291 n n C2' C1' MGP sing 292 n n C2' H2' MGP sing 293 n n O2' HO2' MGP sing 294 n n C1' N9 MGP sing 295 n n C1' H1' MGP sing 296 n n N9 C8 MGP sing 297 n y N9 C4 MGP sing 298 n y C8 N7 MGP doub 299 n y C8 H8 MGP sing 300 n n N7 CM7 MGP sing 301 n n N7 C5 MGP sing 302 n y CM7 HM7 MGP sing 303 n n CM7 HM7A MGP sing 304 n n CM7 HM7B MGP sing 305 n n C5 C6 MGP sing 306 n n C5 C4 MGP doub 307 n y C6 O6 MGP doub 308 n n C6 N1 MGP sing 309 n n N1 C2 MGP sing 310 n n N1 HN1 MGP sing 311 n n C2 N2 MGP sing 312 n n C2 N3 MGP doub 313 n n N2 HN2 MGP sing 314 n n N2 HN2A MGP sing 315 n n N3 C4 MGP sing 316 n n O1A H16 MGP sing 317 n n O1B H17 MGP sing 318 n n O1C H18 MGP sing 319 n n O3C H19 MGP sing 320 n n # _atom_sites.entry_id 5ZJY _atom_sites.fract_transf_matrix[1][1] 0.025126 _atom_sites.fract_transf_matrix[1][2] 0.014506 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.029013 _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] 0.009072 _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 MGP A 1 1001 1001 MGP MGP . D 4 HOH A 1 1101 182 HOH HOH . D 4 HOH A 2 1102 77 HOH HOH . D 4 HOH A 3 1103 168 HOH HOH . D 4 HOH A 4 1104 38 HOH HOH . D 4 HOH A 5 1105 30 HOH HOH . D 4 HOH A 6 1106 79 HOH HOH . D 4 HOH A 7 1107 179 HOH HOH . D 4 HOH A 8 1108 37 HOH HOH . D 4 HOH A 9 1109 180 HOH HOH . D 4 HOH A 10 1110 63 HOH HOH . D 4 HOH A 11 1111 11 HOH HOH . D 4 HOH A 12 1112 47 HOH HOH . D 4 HOH A 13 1113 107 HOH HOH . D 4 HOH A 14 1114 41 HOH HOH . D 4 HOH A 15 1115 50 HOH HOH . D 4 HOH A 16 1116 48 HOH HOH . D 4 HOH A 17 1117 27 HOH HOH . D 4 HOH A 18 1118 108 HOH HOH . D 4 HOH A 19 1119 26 HOH HOH . D 4 HOH A 20 1120 70 HOH HOH . D 4 HOH A 21 1121 58 HOH HOH . D 4 HOH A 22 1122 43 HOH HOH . D 4 HOH A 23 1123 130 HOH HOH . D 4 HOH A 24 1124 9 HOH HOH . D 4 HOH A 25 1125 32 HOH HOH . D 4 HOH A 26 1126 10 HOH HOH . D 4 HOH A 27 1127 42 HOH HOH . D 4 HOH A 28 1128 65 HOH HOH . D 4 HOH A 29 1129 52 HOH HOH . D 4 HOH A 30 1130 33 HOH HOH . D 4 HOH A 31 1131 105 HOH HOH . D 4 HOH A 32 1132 62 HOH HOH . D 4 HOH A 33 1133 55 HOH HOH . D 4 HOH A 34 1134 74 HOH HOH . D 4 HOH A 35 1135 53 HOH HOH . D 4 HOH A 36 1136 18 HOH HOH . D 4 HOH A 37 1137 12 HOH HOH . D 4 HOH A 38 1138 83 HOH HOH . D 4 HOH A 39 1139 115 HOH HOH . D 4 HOH A 40 1140 46 HOH HOH . D 4 HOH A 41 1141 71 HOH HOH . D 4 HOH A 42 1142 102 HOH HOH . D 4 HOH A 43 1143 90 HOH HOH . D 4 HOH A 44 1144 138 HOH HOH . D 4 HOH A 45 1145 80 HOH HOH . D 4 HOH A 46 1146 124 HOH HOH . D 4 HOH A 47 1147 56 HOH HOH . D 4 HOH A 48 1148 3 HOH HOH . D 4 HOH A 49 1149 110 HOH HOH . D 4 HOH A 50 1150 45 HOH HOH . D 4 HOH A 51 1151 29 HOH HOH . D 4 HOH A 52 1152 23 HOH HOH . D 4 HOH A 53 1153 164 HOH HOH . D 4 HOH A 54 1154 14 HOH HOH . D 4 HOH A 55 1155 0 HOH HOH . D 4 HOH A 56 1156 166 HOH HOH . D 4 HOH A 57 1157 20 HOH HOH . D 4 HOH A 58 1158 118 HOH HOH . D 4 HOH A 59 1159 4 HOH HOH . D 4 HOH A 60 1160 36 HOH HOH . D 4 HOH A 61 1161 64 HOH HOH . D 4 HOH A 62 1162 7 HOH HOH . D 4 HOH A 63 1163 140 HOH HOH . D 4 HOH A 64 1164 61 HOH HOH . D 4 HOH A 65 1165 28 HOH HOH . D 4 HOH A 66 1166 144 HOH HOH . D 4 HOH A 67 1167 103 HOH HOH . D 4 HOH A 68 1168 16 HOH HOH . D 4 HOH A 69 1169 22 HOH HOH . D 4 HOH A 70 1170 91 HOH HOH . D 4 HOH A 71 1171 176 HOH HOH . D 4 HOH A 72 1172 69 HOH HOH . D 4 HOH A 73 1173 85 HOH HOH . D 4 HOH A 74 1174 84 HOH HOH . D 4 HOH A 75 1175 17 HOH HOH . D 4 HOH A 76 1176 66 HOH HOH . D 4 HOH A 77 1177 117 HOH HOH . D 4 HOH A 78 1178 97 HOH HOH . D 4 HOH A 79 1179 8 HOH HOH . D 4 HOH A 80 1180 39 HOH HOH . D 4 HOH A 81 1181 129 HOH HOH . D 4 HOH A 82 1182 173 HOH HOH . D 4 HOH A 83 1183 112 HOH HOH . D 4 HOH A 84 1184 24 HOH HOH . D 4 HOH A 85 1185 6 HOH HOH . D 4 HOH A 86 1186 92 HOH HOH . D 4 HOH A 87 1187 100 HOH HOH . D 4 HOH A 88 1188 13 HOH HOH . D 4 HOH A 89 1189 25 HOH HOH . D 4 HOH A 90 1190 81 HOH HOH . D 4 HOH A 91 1191 82 HOH HOH . D 4 HOH A 92 1192 2 HOH HOH . D 4 HOH A 93 1193 184 HOH HOH . D 4 HOH A 94 1194 44 HOH HOH . D 4 HOH A 95 1195 5 HOH HOH . D 4 HOH A 96 1196 21 HOH HOH . D 4 HOH A 97 1197 57 HOH HOH . D 4 HOH A 98 1198 31 HOH HOH . D 4 HOH A 99 1199 111 HOH HOH . D 4 HOH A 100 1200 54 HOH HOH . D 4 HOH A 101 1201 51 HOH HOH . D 4 HOH A 102 1202 86 HOH HOH . D 4 HOH A 103 1203 15 HOH HOH . D 4 HOH A 104 1204 172 HOH HOH . D 4 HOH A 105 1205 154 HOH HOH . D 4 HOH A 106 1206 178 HOH HOH . D 4 HOH A 107 1207 155 HOH HOH . D 4 HOH A 108 1208 73 HOH HOH . D 4 HOH A 109 1209 67 HOH HOH . D 4 HOH A 110 1210 123 HOH HOH . D 4 HOH A 111 1211 121 HOH HOH . D 4 HOH A 112 1212 153 HOH HOH . D 4 HOH A 113 1213 170 HOH HOH . D 4 HOH A 114 1214 174 HOH HOH . D 4 HOH A 115 1215 59 HOH HOH . D 4 HOH A 116 1216 160 HOH HOH . D 4 HOH A 117 1217 161 HOH HOH . D 4 HOH A 118 1218 151 HOH HOH . D 4 HOH A 119 1219 163 HOH HOH . D 4 HOH A 120 1220 165 HOH HOH . D 4 HOH A 121 1221 116 HOH HOH . D 4 HOH A 122 1222 35 HOH HOH . D 4 HOH A 123 1223 175 HOH HOH . D 4 HOH A 124 1224 152 HOH HOH . D 4 HOH A 125 1225 101 HOH HOH . D 4 HOH A 126 1226 133 HOH HOH . D 4 HOH A 127 1227 158 HOH HOH . D 4 HOH A 128 1228 114 HOH HOH . D 4 HOH A 129 1229 119 HOH HOH . D 4 HOH A 130 1230 150 HOH HOH . D 4 HOH A 131 1231 156 HOH HOH . D 4 HOH A 132 1232 94 HOH HOH . D 4 HOH A 133 1233 104 HOH HOH . D 4 HOH A 134 1234 125 HOH HOH . E 4 HOH B 1 101 89 HOH HOH . E 4 HOH B 2 102 131 HOH HOH . E 4 HOH B 3 103 75 HOH HOH . E 4 HOH B 4 104 34 HOH HOH . E 4 HOH B 5 105 159 HOH HOH . E 4 HOH B 6 106 60 HOH HOH . E 4 HOH B 7 107 167 HOH HOH . E 4 HOH B 8 108 19 HOH HOH . E 4 HOH B 9 109 40 HOH HOH . E 4 HOH B 10 110 109 HOH HOH . E 4 HOH B 11 111 87 HOH HOH . E 4 HOH B 12 112 169 HOH HOH . E 4 HOH B 13 113 49 HOH HOH . E 4 HOH B 14 114 98 HOH HOH . E 4 HOH B 15 115 88 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 PA MGP . . . C 3 -27.398 18.999 24.02 1 33.69 ? PA MGP 1001 A 1 HETATM 2 O O1A MGP . . . C 3 -28.205 17.771 23.791 1 34.95 ? O1A MGP 1001 A 1 HETATM 3 O O2A MGP . . . C 3 -25.917 18.999 23.785 1 33.15 ? O2A MGP 1001 A 1 HETATM 4 O O3A MGP . . . C 3 -27.949 20.278 23.229 1 36.66 ? O3A MGP 1001 A 1 HETATM 5 O O5' MGP . . . C 3 -27.608 19.486 25.552 1 32.64 ? O5' MGP 1001 A 1 HETATM 6 P PB MGP . . . C 3 -29.452 20.555 22.698 1 36.35 ? PB MGP 1001 A 1 HETATM 7 O O1B MGP . . . C 3 -30.337 19.4 23.07 1 39.47 ? O1B MGP 1001 A 1 HETATM 8 O O2B MGP . . . C 3 -29.354 20.869 21.242 1 34.3 ? O2B MGP 1001 A 1 HETATM 9 O O3B MGP . . . C 3 -29.803 21.831 23.575 1 43.07 ? O3B MGP 1001 A 1 HETATM 10 P PC MGP . . . C 3 -28.967 23.218 23.58 1 53.35 ? PC MGP 1001 A 1 HETATM 11 O O1C MGP . . . C 3 -27.897 23.115 22.524 1 54.08 ? O1C MGP 1001 A 1 HETATM 12 O O2C MGP . . . C 3 -28.428 23.268 25.001 1 51.77 ? O2C MGP 1001 A 1 HETATM 13 O O3C MGP . . . C 3 -30.032 24.237 23.242 1 49.89 ? O3C MGP 1001 A 1 HETATM 14 C C5' MGP . . . C 3 -28.881 19.44 26.198 1 33.84 ? C5' MGP 1001 A 1 HETATM 15 C C4' MGP . . . C 3 -28.737 19.099 27.681 1 33.1 ? C4' MGP 1001 A 1 HETATM 16 O O4' MGP . . . C 3 -28.242 17.769 27.845 1 31.56 ? O4' MGP 1001 A 1 HETATM 17 C C3' MGP . . . C 3 -27.786 19.987 28.449 1 34.22 ? C3' MGP 1001 A 1 HETATM 18 O O3' MGP . . . C 3 -28.432 21.185 28.891 1 36.07 ? O3' MGP 1001 A 1 HETATM 19 C C2' MGP . . . C 3 -27.353 19.083 29.577 1 34.05 ? C2' MGP 1001 A 1 HETATM 20 O O2' MGP . . . C 3 -28.338 18.963 30.606 1 35.37 ? O2' MGP 1001 A 1 HETATM 21 C C1' MGP . . . C 3 -27.307 17.719 28.925 1 32.42 ? C1' MGP 1001 A 1 HETATM 22 N N9 MGP . . . C 3 -25.938 17.411 28.456 1 30.08 ? N9 MGP 1001 A 1 HETATM 23 C C8 MGP . . . C 3 -25.41 17.504 27.209 1 29.16 ? C8 MGP 1001 A 1 HETATM 24 N N7 MGP . . . C 3 -24.1 17.118 27.205 1 28.82 ? N7 MGP 1001 A 1 HETATM 25 C CM7 MGP . . . C 3 -23.206 17.095 26.025 1 29.36 ? CM7 MGP 1001 A 1 HETATM 26 C C5 MGP . . . C 3 -23.814 16.772 28.452 1 29.02 ? C5 MGP 1001 A 1 HETATM 27 C C6 MGP . . . C 3 -22.597 16.264 29.106 1 28.75 ? C6 MGP 1001 A 1 HETATM 28 O O6 MGP . . . C 3 -21.531 16.07 28.491 1 27.59 ? O6 MGP 1001 A 1 HETATM 29 N N1 MGP . . . C 3 -22.683 16.026 30.426 1 28.07 ? N1 MGP 1001 A 1 HETATM 30 C C2 MGP . . . C 3 -23.817 16.221 31.142 1 29.26 ? C2 MGP 1001 A 1 HETATM 31 N N2 MGP . . . C 3 -23.832 15.964 32.462 1 27.52 ? N2 MGP 1001 A 1 HETATM 32 N N3 MGP . . . C 3 -24.962 16.68 30.598 1 28.27 ? N3 MGP 1001 A 1 HETATM 33 C C4 MGP . . . C 3 -25.005 16.971 29.28 1 29.77 ? C4 MGP 1001 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 33 #