data_1RU2 # _model_server_result.job_id vH1jGnOybCwd5MustYB8pw _model_server_result.datetime_utc '2024-11-24 18:54:54' _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 1ru2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":171}' # _entry.id 1RU2 # _exptl.entry_id 1RU2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL 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 1RU2 _cell.length_a 51.609 _cell.length_b 63.156 _cell.length_c 36.201 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RU2 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 4 _struct_asym.id E _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 OD1 ASP 89 A ASP 95 1_555 B MG MG . A MG 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc2 A OD2 ASP 89 A ASP 95 1_555 C MG MG . A MG 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc3 A OD1 ASP 91 A ASP 97 1_555 B MG MG . A MG 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc4 A OD2 ASP 91 A ASP 97 1_555 C MG MG . A MG 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc5 B MG MG . A MG 161 1_555 E O1B APC . A APC 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc6 B MG MG . A MG 161 1_555 E O1A APC . A APC 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc7 B MG MG . A MG 161 1_555 G O HOH . A HOH 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc8 B MG MG . A MG 161 1_555 G O HOH . A HOH 249 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc9 C MG MG . A MG 162 1_555 E O3G APC . A APC 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc10 C MG MG . A MG 162 1_555 E O1B APC . A APC 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc11 C MG MG . A MG 162 1_555 F O6A HHR . A HHR 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc12 C MG MG . A MG 162 1_555 G O HOH . A HOH 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" # 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 APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 1RU2 _atom_sites.fract_transf_matrix[1][1] 0.019376 _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] 0.015834 _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] 0.027624 _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 1 161 161 MG MG . C 2 MG A 1 162 162 MG MG . D 3 CL A 1 163 163 CL CL . E 4 APC A 1 171 171 APC APC . F 5 HHR A 1 181 181 HHR HHR . G 6 HOH A 1 201 201 HOH HOH . G 6 HOH A 2 202 202 HOH HOH . G 6 HOH A 3 203 203 HOH HOH . G 6 HOH A 4 204 204 HOH HOH . G 6 HOH A 5 205 205 HOH HOH . G 6 HOH A 6 206 206 HOH HOH . G 6 HOH A 7 207 207 HOH HOH . G 6 HOH A 8 208 208 HOH HOH . G 6 HOH A 9 209 209 HOH HOH . G 6 HOH A 10 210 210 HOH HOH . G 6 HOH A 11 211 211 HOH HOH . G 6 HOH A 12 212 212 HOH HOH . G 6 HOH A 13 213 213 HOH HOH . G 6 HOH A 14 214 214 HOH HOH . G 6 HOH A 15 215 215 HOH HOH . G 6 HOH A 16 216 216 HOH HOH . G 6 HOH A 17 217 217 HOH HOH . G 6 HOH A 18 218 218 HOH HOH . G 6 HOH A 19 219 219 HOH HOH . G 6 HOH A 20 220 220 HOH HOH . G 6 HOH A 21 221 221 HOH HOH . G 6 HOH A 22 222 222 HOH HOH . G 6 HOH A 23 223 223 HOH HOH . G 6 HOH A 24 224 224 HOH HOH . G 6 HOH A 25 225 225 HOH HOH . G 6 HOH A 26 226 226 HOH HOH . G 6 HOH A 27 227 227 HOH HOH . G 6 HOH A 28 228 228 HOH HOH . G 6 HOH A 29 229 229 HOH HOH . G 6 HOH A 30 230 230 HOH HOH . G 6 HOH A 31 231 231 HOH HOH . G 6 HOH A 32 232 232 HOH HOH . G 6 HOH A 33 233 233 HOH HOH . G 6 HOH A 34 234 234 HOH HOH . G 6 HOH A 35 235 235 HOH HOH . G 6 HOH A 36 236 236 HOH HOH . G 6 HOH A 37 237 237 HOH HOH . G 6 HOH A 38 238 238 HOH HOH . G 6 HOH A 39 239 239 HOH HOH . G 6 HOH A 40 240 240 HOH HOH . G 6 HOH A 41 241 241 HOH HOH . G 6 HOH A 42 242 242 HOH HOH . G 6 HOH A 43 243 243 HOH HOH . G 6 HOH A 44 244 244 HOH HOH . G 6 HOH A 45 245 245 HOH HOH . G 6 HOH A 46 246 246 HOH HOH . G 6 HOH A 47 247 247 HOH HOH . G 6 HOH A 48 248 248 HOH HOH . G 6 HOH A 49 249 249 HOH HOH . G 6 HOH A 50 250 250 HOH HOH . G 6 HOH A 51 251 251 HOH HOH . G 6 HOH A 52 252 252 HOH HOH . G 6 HOH A 53 253 253 HOH HOH . G 6 HOH A 54 254 254 HOH HOH . G 6 HOH A 55 255 255 HOH HOH . G 6 HOH A 56 256 256 HOH HOH . G 6 HOH A 57 257 257 HOH HOH . G 6 HOH A 58 258 258 HOH HOH . G 6 HOH A 59 259 259 HOH HOH . G 6 HOH A 60 260 260 HOH HOH . G 6 HOH A 61 261 261 HOH HOH . G 6 HOH A 62 262 262 HOH HOH . G 6 HOH A 63 263 263 HOH HOH . G 6 HOH A 64 264 264 HOH HOH . G 6 HOH A 65 265 265 HOH HOH . G 6 HOH A 66 266 266 HOH HOH . G 6 HOH A 67 267 267 HOH HOH . G 6 HOH A 68 268 268 HOH HOH . G 6 HOH A 69 269 269 HOH HOH . G 6 HOH A 70 270 270 HOH HOH . G 6 HOH A 71 271 271 HOH HOH . G 6 HOH A 72 272 272 HOH HOH . G 6 HOH A 73 273 273 HOH HOH . G 6 HOH A 74 274 274 HOH HOH . G 6 HOH A 75 275 275 HOH HOH . G 6 HOH A 76 276 276 HOH HOH . G 6 HOH A 77 277 277 HOH HOH . G 6 HOH A 78 278 278 HOH HOH . G 6 HOH A 79 279 279 HOH HOH . G 6 HOH A 80 280 280 HOH HOH . G 6 HOH A 81 281 281 HOH HOH . G 6 HOH A 82 282 282 HOH HOH . G 6 HOH A 83 283 283 HOH HOH . G 6 HOH A 84 284 284 HOH HOH . G 6 HOH A 85 285 285 HOH HOH . G 6 HOH A 86 286 286 HOH HOH . G 6 HOH A 87 287 287 HOH HOH . G 6 HOH A 88 288 288 HOH HOH . G 6 HOH A 89 289 289 HOH HOH . G 6 HOH A 90 290 290 HOH HOH . G 6 HOH A 91 291 291 HOH HOH . G 6 HOH A 92 292 292 HOH HOH . G 6 HOH A 93 293 293 HOH HOH . G 6 HOH A 94 294 294 HOH HOH . G 6 HOH A 95 295 295 HOH HOH . G 6 HOH A 96 296 296 HOH HOH . G 6 HOH A 97 297 297 HOH HOH . G 6 HOH A 98 298 298 HOH HOH . G 6 HOH A 99 299 299 HOH HOH . G 6 HOH A 100 300 300 HOH HOH . G 6 HOH A 101 301 301 HOH HOH . G 6 HOH A 102 302 302 HOH HOH . G 6 HOH A 103 303 303 HOH HOH . G 6 HOH A 104 304 304 HOH HOH . G 6 HOH A 105 305 305 HOH HOH . G 6 HOH A 106 306 306 HOH HOH . G 6 HOH A 107 307 307 HOH HOH . G 6 HOH A 108 308 308 HOH HOH . G 6 HOH A 109 309 309 HOH HOH . G 6 HOH A 110 310 310 HOH HOH . G 6 HOH A 111 311 311 HOH HOH . G 6 HOH A 112 312 312 HOH HOH . G 6 HOH A 113 313 313 HOH HOH . G 6 HOH A 114 314 314 HOH HOH . G 6 HOH A 115 315 315 HOH HOH . G 6 HOH A 116 316 316 HOH HOH . G 6 HOH A 117 317 317 HOH HOH . G 6 HOH A 118 318 318 HOH HOH . G 6 HOH A 119 319 319 HOH HOH . G 6 HOH A 120 320 320 HOH HOH . G 6 HOH A 121 321 321 HOH HOH . G 6 HOH A 122 322 322 HOH HOH . G 6 HOH A 123 323 323 HOH HOH . G 6 HOH A 124 324 324 HOH HOH . G 6 HOH A 125 325 325 HOH HOH . G 6 HOH A 126 326 326 HOH HOH . G 6 HOH A 127 327 327 HOH HOH . G 6 HOH A 128 328 328 HOH HOH . G 6 HOH A 129 329 329 HOH HOH . G 6 HOH A 130 330 330 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 APC . . . E 4 3.235 18.353 10.055 1 23.72 ? PG APC 171 A 1 HETATM 2 O O1G APC . . . E 4 2.807 16.957 10.316 1 26.97 ? O1G APC 171 A 1 HETATM 3 O O2G APC . . . E 4 2.19 19.138 9.291 1 26.13 ? O2G APC 171 A 1 HETATM 4 O O3G APC . . . E 4 4.611 18.366 9.416 1 19.59 ? O3G APC 171 A 1 HETATM 5 P PB APC . . . E 4 4.438 18.941 12.602 1 23.68 ? PB APC 171 A 1 HETATM 6 O O1B APC . . . E 4 5.641 18.342 11.93 1 23.85 ? O1B APC 171 A 1 HETATM 7 O O2B APC . . . E 4 4.61 20.203 13.373 1 25.32 ? O2B APC 171 A 1 HETATM 8 O O3B APC . . . E 4 3.383 19.18 11.433 1 23.62 ? O3B APC 171 A 1 HETATM 9 P PA APC . . . E 4 4.48 17.592 15.232 1 24.7 ? PA APC 171 A 1 HETATM 10 O O1A APC . . . E 4 5.979 17.607 14.968 1 25.5 ? O1A APC 171 A 1 HETATM 11 O O2A APC . . . E 4 4.013 18.547 16.264 1 26.41 ? O2A APC 171 A 1 HETATM 12 C C3A APC . . . E 4 3.65 17.742 13.672 1 33.26 ? C3A APC 171 A 1 HETATM 13 O O5' APC . . . E 4 4.255 16.099 15.765 1 24.8 ? O5' APC 171 A 1 HETATM 14 C C5' APC . . . E 4 2.943 15.713 16.31 1 27.58 ? C5' APC 171 A 1 HETATM 15 C C4' APC . . . E 4 2.755 14.236 16.138 1 28.63 ? C4' APC 171 A 1 HETATM 16 O O4' APC . . . E 4 2.802 13.788 14.783 1 27.45 ? O4' APC 171 A 1 HETATM 17 C C3' APC . . . E 4 3.657 13.368 16.932 1 28.53 ? C3' APC 171 A 1 HETATM 18 O O3' APC . . . E 4 3.261 13.365 18.27 1 37.31 ? O3' APC 171 A 1 HETATM 19 C C2' APC . . . E 4 3.564 12.051 16.235 1 27.32 ? C2' APC 171 A 1 HETATM 20 O O2' APC . . . E 4 2.866 11.008 16.978 1 29.85 ? O2' APC 171 A 1 HETATM 21 C C1' APC . . . E 4 2.796 12.336 14.964 1 27.29 ? C1' APC 171 A 1 HETATM 22 N N9 APC . . . E 4 3.268 11.823 13.689 1 27 ? N9 APC 171 A 1 HETATM 23 C C8 APC . . . E 4 2.335 11.165 12.825 1 26.34 ? C8 APC 171 A 1 HETATM 24 N N7 APC . . . E 4 2.963 10.779 11.726 1 23.71 ? N7 APC 171 A 1 HETATM 25 C C5 APC . . . E 4 4.307 11.197 11.898 1 21.11 ? C5 APC 171 A 1 HETATM 26 C C6 APC . . . E 4 5.38 11.038 11.034 1 19 ? C6 APC 171 A 1 HETATM 27 N N6 APC . . . E 4 5.354 10.459 9.875 1 19.75 ? N6 APC 171 A 1 HETATM 28 N N1 APC . . . E 4 6.629 11.554 11.45 1 20.49 ? N1 APC 171 A 1 HETATM 29 C C2 APC . . . E 4 6.729 12.154 12.618 1 18.73 ? C2 APC 171 A 1 HETATM 30 N N3 APC . . . E 4 5.676 12.368 13.581 1 21.2 ? N3 APC 171 A 1 HETATM 31 C C4 APC . . . E 4 4.475 11.833 13.102 1 23.49 ? C4 APC 171 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 210 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #