data_5YRO # _model_server_result.job_id -pmYeQ0kwTxHDYqxszDkog _model_server_result.datetime_utc '2024-11-21 16:18:30' _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 5yro # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 5YRO # _exptl.entry_id 5YRO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "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 90 _cell.entry_id 5YRO _cell.length_a 105.259 _cell.length_b 105.259 _cell.length_c 307.425 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YRO _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,H,I,J,K,L,M,N,O _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 4 _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 OG1 THR 24 A THR 24 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc2 D O2G GTP . A GTP 301 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc3 D O1B GTP . A GTP 301 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc4 E MG MG . A MG 302 1_555 M O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc5 E MG MG . A MG 302 1_555 M O HOH . A HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "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 PG O1G GTP doub 151 n n PG O2G GTP sing 152 n n PG O3G GTP sing 153 n n PG O3B GTP sing 154 n n O2G HOG2 GTP sing 155 n n O3G HOG3 GTP sing 156 n n O3B PB GTP sing 157 n n PB O1B GTP doub 158 n n PB O2B GTP sing 159 n n PB O3A GTP sing 160 n n O2B HOB2 GTP sing 161 n n O3A PA GTP sing 162 n n PA O1A GTP doub 163 n n PA O2A GTP sing 164 n n PA O5' GTP sing 165 n n O2A HOA2 GTP sing 166 n n O5' C5' GTP sing 167 n n C5' C4' GTP sing 168 n n C5' H5' GTP sing 169 n n C5' "H5''" GTP sing 170 n n C4' O4' GTP sing 171 n n C4' C3' GTP sing 172 n n C4' H4' GTP sing 173 n n O4' C1' GTP sing 174 n n C3' O3' GTP sing 175 n n C3' C2' GTP sing 176 n n C3' H3' GTP sing 177 n n O3' HO3' GTP sing 178 n n C2' O2' GTP sing 179 n n C2' C1' GTP sing 180 n n C2' H2' GTP sing 181 n n O2' HO2' GTP sing 182 n n C1' N9 GTP sing 183 n n C1' H1' GTP sing 184 n n N9 C8 GTP sing 185 n y N9 C4 GTP sing 186 n y C8 N7 GTP doub 187 n y C8 H8 GTP sing 188 n n N7 C5 GTP sing 189 n y C5 C6 GTP sing 190 n n C5 C4 GTP doub 191 n y C6 O6 GTP doub 192 n n C6 N1 GTP sing 193 n n N1 C2 GTP sing 194 n n N1 HN1 GTP sing 195 n n C2 N2 GTP sing 196 n n C2 N3 GTP doub 197 n n N2 HN21 GTP sing 198 n n N2 HN22 GTP sing 199 n n N3 C4 GTP sing 200 n n # _atom_sites.entry_id 5YRO _atom_sites.fract_transf_matrix[1][1] 0.0095 _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] 0.0095 _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] 0.003253 _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 D 4 GTP A 1 301 1177 GTP GTP . E 5 MG A 1 302 302 MG MG . F 6 EDO A 1 303 303 EDO EDO . G 5 MG A 1 304 1 MG MG . H 7 GOL C 1 1101 1102 GOL GOL . I 8 CL C 1 1102 1104 CL CL . J 8 CL C 1 1103 1105 CL CL . K 8 CL C 1 1104 1106 CL CL . L 8 CL C 1 1105 1107 CL CL . M 9 HOH A 1 401 92 HOH HOH . M 9 HOH A 2 402 114 HOH HOH . M 9 HOH A 3 403 1 HOH HOH . M 9 HOH A 4 404 83 HOH HOH . M 9 HOH A 5 405 119 HOH HOH . M 9 HOH A 6 406 12 HOH HOH . M 9 HOH A 7 407 3 HOH HOH . M 9 HOH A 8 408 4 HOH HOH . M 9 HOH A 9 409 6 HOH HOH . M 9 HOH A 10 410 122 HOH HOH . M 9 HOH A 11 411 115 HOH HOH . M 9 HOH A 12 412 15 HOH HOH . M 9 HOH A 13 413 13 HOH HOH . M 9 HOH A 14 414 16 HOH HOH . M 9 HOH A 15 415 121 HOH HOH . M 9 HOH A 16 416 34 HOH HOH . M 9 HOH A 17 417 2 HOH HOH . M 9 HOH A 18 418 17 HOH HOH . M 9 HOH A 19 419 109 HOH HOH . M 9 HOH A 20 420 8 HOH HOH . M 9 HOH A 21 421 7 HOH HOH . M 9 HOH A 22 422 5 HOH HOH . M 9 HOH A 23 423 18 HOH HOH . M 9 HOH A 24 424 20 HOH HOH . M 9 HOH A 25 425 9 HOH HOH . M 9 HOH A 26 426 14 HOH HOH . M 9 HOH A 27 427 19 HOH HOH . M 9 HOH A 28 428 95 HOH HOH . M 9 HOH A 29 429 88 HOH HOH . N 9 HOH B 1 301 90 HOH HOH . N 9 HOH B 2 302 116 HOH HOH . N 9 HOH B 3 303 23 HOH HOH . N 9 HOH B 4 304 22 HOH HOH . N 9 HOH B 5 305 104 HOH HOH . N 9 HOH B 6 306 106 HOH HOH . N 9 HOH B 7 307 105 HOH HOH . N 9 HOH B 8 308 21 HOH HOH . N 9 HOH B 9 309 93 HOH HOH . N 9 HOH B 10 310 113 HOH HOH . N 9 HOH B 11 311 82 HOH HOH . O 9 HOH C 1 1201 40 HOH HOH . O 9 HOH C 2 1202 71 HOH HOH . O 9 HOH C 3 1203 47 HOH HOH . O 9 HOH C 4 1204 66 HOH HOH . O 9 HOH C 5 1205 11 HOH HOH . O 9 HOH C 6 1206 37 HOH HOH . O 9 HOH C 7 1207 96 HOH HOH . O 9 HOH C 8 1208 118 HOH HOH . O 9 HOH C 9 1209 86 HOH HOH . O 9 HOH C 10 1210 42 HOH HOH . O 9 HOH C 11 1211 43 HOH HOH . O 9 HOH C 12 1212 112 HOH HOH . O 9 HOH C 13 1213 100 HOH HOH . O 9 HOH C 14 1214 79 HOH HOH . O 9 HOH C 15 1215 54 HOH HOH . O 9 HOH C 16 1216 35 HOH HOH . O 9 HOH C 17 1217 41 HOH HOH . O 9 HOH C 18 1218 91 HOH HOH . O 9 HOH C 19 1219 58 HOH HOH . O 9 HOH C 20 1220 99 HOH HOH . O 9 HOH C 21 1221 49 HOH HOH . O 9 HOH C 22 1222 120 HOH HOH . O 9 HOH C 23 1223 107 HOH HOH . O 9 HOH C 24 1224 61 HOH HOH . O 9 HOH C 25 1225 52 HOH HOH . O 9 HOH C 26 1226 45 HOH HOH . O 9 HOH C 27 1227 84 HOH HOH . O 9 HOH C 28 1228 31 HOH HOH . O 9 HOH C 29 1229 97 HOH HOH . O 9 HOH C 30 1230 81 HOH HOH . O 9 HOH C 31 1231 110 HOH HOH . O 9 HOH C 32 1232 10 HOH HOH . O 9 HOH C 33 1233 85 HOH HOH . O 9 HOH C 34 1234 117 HOH HOH . O 9 HOH C 35 1235 89 HOH HOH . O 9 HOH C 36 1236 108 HOH HOH . O 9 HOH C 37 1237 27 HOH HOH . O 9 HOH C 38 1238 77 HOH HOH . O 9 HOH C 39 1239 59 HOH HOH . O 9 HOH C 40 1240 69 HOH HOH . O 9 HOH C 41 1241 36 HOH HOH . O 9 HOH C 42 1242 50 HOH HOH . O 9 HOH C 43 1243 38 HOH HOH . O 9 HOH C 44 1244 53 HOH HOH . O 9 HOH C 45 1245 29 HOH HOH . O 9 HOH C 46 1246 39 HOH HOH . O 9 HOH C 47 1247 67 HOH HOH . O 9 HOH C 48 1248 32 HOH HOH . O 9 HOH C 49 1249 28 HOH HOH . O 9 HOH C 50 1250 103 HOH HOH . O 9 HOH C 51 1251 56 HOH HOH . O 9 HOH C 52 1252 30 HOH HOH . O 9 HOH C 53 1253 111 HOH HOH . O 9 HOH C 54 1254 51 HOH HOH . O 9 HOH C 55 1255 44 HOH HOH . O 9 HOH C 56 1256 80 HOH HOH . O 9 HOH C 57 1257 46 HOH HOH . O 9 HOH C 58 1258 62 HOH HOH . O 9 HOH C 59 1259 101 HOH HOH . O 9 HOH C 60 1260 24 HOH HOH . O 9 HOH C 61 1261 26 HOH HOH . O 9 HOH C 62 1262 76 HOH HOH . O 9 HOH C 63 1263 65 HOH HOH . O 9 HOH C 64 1264 57 HOH HOH . O 9 HOH C 65 1265 25 HOH HOH . O 9 HOH C 66 1266 87 HOH HOH . O 9 HOH C 67 1267 75 HOH HOH . O 9 HOH C 68 1268 72 HOH HOH . O 9 HOH C 69 1269 55 HOH HOH . O 9 HOH C 70 1270 68 HOH HOH . O 9 HOH C 71 1271 70 HOH HOH . O 9 HOH C 72 1272 102 HOH HOH . O 9 HOH C 73 1273 73 HOH HOH . O 9 HOH C 74 1274 74 HOH HOH . O 9 HOH C 75 1275 98 HOH HOH . O 9 HOH C 76 1276 48 HOH HOH . O 9 HOH C 77 1277 33 HOH HOH . O 9 HOH C 78 1278 94 HOH HOH . O 9 HOH C 79 1279 78 HOH HOH . O 9 HOH C 80 1280 60 HOH HOH . O 9 HOH C 81 1281 64 HOH HOH . O 9 HOH C 82 1282 63 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 PG GTP . . . D 4 7.324 37.638 28.321 1 63.47 ? PG GTP 301 A 1 HETATM 2 O O1G GTP . . . D 4 7.292 36.452 27.516 1 63.75 ? O1G GTP 301 A 1 HETATM 3 O O2G GTP . . . D 4 8.465 38.517 28.134 1 62.07 ? O2G GTP 301 A 1 HETATM 4 O O3G GTP . . . D 4 7.026 37.358 29.698 1 64.07 ? O3G GTP 301 A 1 HETATM 5 O O3B GTP . . . D 4 6.152 38.505 27.717 1 62.09 ? O3B GTP 301 A 1 HETATM 6 P PB GTP . . . D 4 5.673 39.959 28.095 1 59.15 ? PB GTP 301 A 1 HETATM 7 O O1B GTP . . . D 4 6.817 40.794 28.32 1 60.19 ? O1B GTP 301 A 1 HETATM 8 O O2B GTP . . . D 4 4.687 39.937 29.14 1 60.39 ? O2B GTP 301 A 1 HETATM 9 O O3A GTP . . . D 4 4.96 40.422 26.782 1 60.05 ? O3A GTP 301 A 1 HETATM 10 P PA GTP . . . D 4 5.4 41.538 25.787 1 59.63 ? PA GTP 301 A 1 HETATM 11 O O1A GTP . . . D 4 6.713 41.264 25.27 1 61.04 ? O1A GTP 301 A 1 HETATM 12 O O2A GTP . . . D 4 5.035 42.844 26.276 1 59.78 ? O2A GTP 301 A 1 HETATM 13 O O5' GTP . . . D 4 4.436 41.323 24.609 1 59.64 ? O5' GTP 301 A 1 HETATM 14 C C5' GTP . . . D 4 3.066 41.498 24.838 1 59.52 ? C5' GTP 301 A 1 HETATM 15 C C4' GTP . . . D 4 2.316 41.55 23.538 1 59.82 ? C4' GTP 301 A 1 HETATM 16 O O4' GTP . . . D 4 1.054 42.109 23.801 1 57.35 ? O4' GTP 301 A 1 HETATM 17 C C3' GTP . . . D 4 2.992 42.489 22.586 1 59.81 ? C3' GTP 301 A 1 HETATM 18 O O3' GTP . . . D 4 2.65 42.147 21.271 1 61.22 ? O3' GTP 301 A 1 HETATM 19 C C2' GTP . . . D 4 2.301 43.774 22.844 1 58.93 ? C2' GTP 301 A 1 HETATM 20 O O2' GTP . . . D 4 2.312 44.534 21.668 1 61.15 ? O2' GTP 301 A 1 HETATM 21 C C1' GTP . . . D 4 0.906 43.355 23.175 1 58.17 ? C1' GTP 301 A 1 HETATM 22 N N9 GTP . . . D 4 0.316 44.271 24.145 1 57.65 ? N9 GTP 301 A 1 HETATM 23 C C8 GTP . . . D 4 0.883 44.661 25.262 1 57.36 ? C8 GTP 301 A 1 HETATM 24 N N7 GTP . . . D 4 0.093 45.482 25.936 1 56.45 ? N7 GTP 301 A 1 HETATM 25 C C5 GTP . . . D 4 -1.017 45.613 25.25 1 55.94 ? C5 GTP 301 A 1 HETATM 26 C C6 GTP . . . D 4 -2.259 46.346 25.416 1 56.21 ? C6 GTP 301 A 1 HETATM 27 O O6 GTP . . . D 4 -2.455 47.048 26.378 1 57.86 ? O6 GTP 301 A 1 HETATM 28 N N1 GTP . . . D 4 -3.161 46.242 24.494 1 56.95 ? N1 GTP 301 A 1 HETATM 29 C C2 GTP . . . D 4 -2.957 45.486 23.437 1 56.95 ? C2 GTP 301 A 1 HETATM 30 N N2 GTP . . . D 4 -3.933 45.434 22.545 1 56.2 ? N2 GTP 301 A 1 HETATM 31 N N3 GTP . . . D 4 -1.853 44.783 23.203 1 56.46 ? N3 GTP 301 A 1 HETATM 32 C C4 GTP . . . D 4 -0.863 44.807 24.07 1 56.18 ? C4 GTP 301 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 66 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #