data_4EPW # _model_server_result.job_id P_Si5wAsZfwZ7jUwHvSqmw _model_server_result.datetime_utc '2024-11-14 10:55:46' _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 4epw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4EPW # _exptl.entry_id 4EPW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 4EPW _cell.length_a 39.219 _cell.length_b 41.924 _cell.length_c 91.448 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EPW _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 2 _struct_asym.id B _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 OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc2 B O2B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc3 C MG MG . A MG 202 1_555 E O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-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 PB O1B GDP doub 119 n n PB O2B GDP sing 120 n n PB O3B GDP sing 121 n n PB O3A GDP sing 122 n n O2B HOB2 GDP sing 123 n n O3B HOB3 GDP sing 124 n n O3A PA GDP sing 125 n n PA O1A GDP doub 126 n n PA O2A GDP sing 127 n n PA O5' GDP sing 128 n n O2A HOA2 GDP sing 129 n n O5' C5' GDP sing 130 n n C5' C4' GDP sing 131 n n C5' H5' GDP sing 132 n n C5' "H5''" GDP sing 133 n n C4' O4' GDP sing 134 n n C4' C3' GDP sing 135 n n C4' H4' GDP sing 136 n n O4' C1' GDP sing 137 n n C3' O3' GDP sing 138 n n C3' C2' GDP sing 139 n n C3' H3' GDP sing 140 n n O3' HO3' GDP sing 141 n n C2' O2' GDP sing 142 n n C2' C1' GDP sing 143 n n C2' H2' GDP sing 144 n n O2' HO2' GDP sing 145 n n C1' N9 GDP sing 146 n n C1' H1' GDP sing 147 n n N9 C8 GDP sing 148 n y N9 C4 GDP sing 149 n y C8 N7 GDP doub 150 n y C8 H8 GDP sing 151 n n N7 C5 GDP sing 152 n y C5 C6 GDP sing 153 n n C5 C4 GDP doub 154 n y C6 O6 GDP doub 155 n n C6 N1 GDP sing 156 n n N1 C2 GDP sing 157 n n N1 HN1 GDP sing 158 n n C2 N2 GDP sing 159 n n C2 N3 GDP doub 160 n n N2 HN21 GDP sing 161 n n N2 HN22 GDP sing 162 n n N3 C4 GDP sing 163 n n # _atom_sites.entry_id 4EPW _atom_sites.fract_transf_matrix[1][1] 0.025498 _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] 0.023853 _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] 0.010935 _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 GDP A 1 201 201 GDP GDP . C 3 MG A 1 202 301 MG MG . D 4 0QV A 1 203 401 0QV JPB . E 5 HOH A 1 301 1 HOH HOH . E 5 HOH A 2 302 2 HOH HOH . E 5 HOH A 3 303 3 HOH HOH . E 5 HOH A 4 304 4 HOH HOH . E 5 HOH A 5 305 5 HOH HOH . E 5 HOH A 6 306 6 HOH HOH . E 5 HOH A 7 307 7 HOH HOH . E 5 HOH A 8 308 8 HOH HOH . E 5 HOH A 9 309 9 HOH HOH . E 5 HOH A 10 310 10 HOH HOH . E 5 HOH A 11 311 11 HOH HOH . E 5 HOH A 12 312 12 HOH HOH . E 5 HOH A 13 313 13 HOH HOH . E 5 HOH A 14 314 14 HOH HOH . E 5 HOH A 15 315 15 HOH HOH . E 5 HOH A 16 316 16 HOH HOH . E 5 HOH A 17 317 17 HOH HOH . E 5 HOH A 18 318 18 HOH HOH . E 5 HOH A 19 319 19 HOH HOH . E 5 HOH A 20 320 20 HOH HOH . E 5 HOH A 21 321 21 HOH HOH . E 5 HOH A 22 322 22 HOH HOH . E 5 HOH A 23 323 23 HOH HOH . E 5 HOH A 24 324 24 HOH HOH . E 5 HOH A 25 325 25 HOH HOH . E 5 HOH A 26 326 26 HOH HOH . E 5 HOH A 27 327 27 HOH HOH . E 5 HOH A 28 328 28 HOH HOH . E 5 HOH A 29 329 29 HOH HOH . E 5 HOH A 30 330 30 HOH HOH . E 5 HOH A 31 331 31 HOH HOH . E 5 HOH A 32 332 32 HOH HOH . E 5 HOH A 33 333 33 HOH HOH . E 5 HOH A 34 334 34 HOH HOH . E 5 HOH A 35 335 35 HOH HOH . E 5 HOH A 36 336 36 HOH HOH . E 5 HOH A 37 337 37 HOH HOH . E 5 HOH A 38 338 38 HOH HOH . E 5 HOH A 39 339 39 HOH HOH . E 5 HOH A 40 340 40 HOH HOH . E 5 HOH A 41 341 41 HOH HOH . E 5 HOH A 42 342 42 HOH HOH . E 5 HOH A 43 343 43 HOH HOH . E 5 HOH A 44 344 44 HOH HOH . E 5 HOH A 45 345 45 HOH HOH . E 5 HOH A 46 346 46 HOH HOH . E 5 HOH A 47 347 47 HOH HOH . E 5 HOH A 48 348 48 HOH HOH . E 5 HOH A 49 349 49 HOH HOH . E 5 HOH A 50 350 50 HOH HOH . E 5 HOH A 51 351 51 HOH HOH . E 5 HOH A 52 352 52 HOH HOH . E 5 HOH A 53 353 53 HOH HOH . E 5 HOH A 54 354 54 HOH HOH . E 5 HOH A 55 355 55 HOH HOH . E 5 HOH A 56 356 56 HOH HOH . E 5 HOH A 57 357 57 HOH HOH . E 5 HOH A 58 358 58 HOH HOH . E 5 HOH A 59 359 59 HOH HOH . E 5 HOH A 60 360 60 HOH HOH . E 5 HOH A 61 361 61 HOH HOH . E 5 HOH A 62 362 62 HOH HOH . E 5 HOH A 63 363 63 HOH HOH . E 5 HOH A 64 364 64 HOH HOH . E 5 HOH A 65 365 65 HOH HOH . E 5 HOH A 66 366 66 HOH HOH . E 5 HOH A 67 367 67 HOH HOH . E 5 HOH A 68 368 68 HOH HOH . E 5 HOH A 69 369 69 HOH HOH . E 5 HOH A 70 370 70 HOH HOH . E 5 HOH A 71 371 71 HOH HOH . E 5 HOH A 72 372 72 HOH HOH . E 5 HOH A 73 373 73 HOH HOH . E 5 HOH A 74 374 74 HOH HOH . E 5 HOH A 75 375 75 HOH HOH . E 5 HOH A 76 376 76 HOH HOH . E 5 HOH A 77 377 77 HOH HOH . E 5 HOH A 78 378 78 HOH HOH . E 5 HOH A 79 379 79 HOH HOH . E 5 HOH A 80 380 80 HOH HOH . E 5 HOH A 81 381 81 HOH HOH . E 5 HOH A 82 382 82 HOH HOH . E 5 HOH A 83 383 83 HOH HOH . E 5 HOH A 84 384 84 HOH HOH . E 5 HOH A 85 385 85 HOH HOH . E 5 HOH A 86 386 86 HOH HOH . E 5 HOH A 87 387 87 HOH HOH . E 5 HOH A 88 388 88 HOH HOH . E 5 HOH A 89 389 89 HOH HOH . E 5 HOH A 90 390 90 HOH HOH . E 5 HOH A 91 391 91 HOH HOH . E 5 HOH A 92 392 92 HOH HOH . E 5 HOH A 93 393 93 HOH HOH . E 5 HOH A 94 394 94 HOH HOH . E 5 HOH A 95 395 95 HOH HOH . E 5 HOH A 96 396 96 HOH HOH . E 5 HOH A 97 397 97 HOH HOH . E 5 HOH A 98 398 98 HOH HOH . E 5 HOH A 99 399 99 HOH HOH . E 5 HOH A 100 400 100 HOH HOH . E 5 HOH A 101 401 101 HOH HOH . E 5 HOH A 102 402 102 HOH HOH . E 5 HOH A 103 403 103 HOH HOH . E 5 HOH A 104 404 104 HOH HOH . E 5 HOH A 105 405 105 HOH HOH . E 5 HOH A 106 406 106 HOH HOH . E 5 HOH A 107 407 107 HOH HOH . E 5 HOH A 108 408 108 HOH HOH . E 5 HOH A 109 409 109 HOH HOH . E 5 HOH A 110 410 110 HOH HOH . E 5 HOH A 111 411 111 HOH HOH . E 5 HOH A 112 412 112 HOH HOH . E 5 HOH A 113 413 113 HOH HOH . E 5 HOH A 114 414 114 HOH HOH . E 5 HOH A 115 415 115 HOH HOH . E 5 HOH A 116 416 116 HOH HOH . E 5 HOH A 117 417 117 HOH HOH . E 5 HOH A 118 418 118 HOH HOH . E 5 HOH A 119 419 119 HOH HOH . E 5 HOH A 120 420 120 HOH HOH . E 5 HOH A 121 421 121 HOH HOH . E 5 HOH A 122 422 122 HOH HOH . E 5 HOH A 123 423 123 HOH HOH . E 5 HOH A 124 424 124 HOH HOH . E 5 HOH A 125 425 125 HOH HOH . E 5 HOH A 126 426 126 HOH HOH . E 5 HOH A 127 427 127 HOH HOH . E 5 HOH A 128 428 128 HOH HOH . E 5 HOH A 129 429 129 HOH HOH . E 5 HOH A 130 430 130 HOH HOH . E 5 HOH A 131 431 131 HOH HOH . E 5 HOH A 132 432 132 HOH HOH . E 5 HOH A 133 433 133 HOH HOH . E 5 HOH A 134 434 134 HOH HOH . E 5 HOH A 135 435 135 HOH HOH . E 5 HOH A 136 436 136 HOH HOH . E 5 HOH A 137 437 137 HOH HOH . E 5 HOH A 138 438 138 HOH HOH . E 5 HOH A 139 439 139 HOH HOH . E 5 HOH A 140 440 140 HOH HOH . E 5 HOH A 141 441 141 HOH HOH . E 5 HOH A 142 442 142 HOH HOH . E 5 HOH A 143 443 143 HOH HOH . E 5 HOH A 144 444 144 HOH HOH . E 5 HOH A 145 445 145 HOH HOH . E 5 HOH A 146 446 146 HOH HOH . E 5 HOH A 147 447 147 HOH HOH . E 5 HOH A 148 448 148 HOH HOH . E 5 HOH A 149 449 149 HOH HOH . E 5 HOH A 150 450 150 HOH HOH . E 5 HOH A 151 451 151 HOH HOH . E 5 HOH A 152 452 152 HOH HOH . E 5 HOH A 153 453 153 HOH HOH . E 5 HOH A 154 454 154 HOH HOH . E 5 HOH A 155 455 155 HOH HOH . E 5 HOH A 156 456 156 HOH HOH . E 5 HOH A 157 457 157 HOH HOH . E 5 HOH A 158 458 158 HOH HOH . E 5 HOH A 159 459 159 HOH HOH . E 5 HOH A 160 460 160 HOH HOH . E 5 HOH A 161 461 161 HOH HOH . E 5 HOH A 162 462 162 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 GDP . . . B 2 -10.197 -7.352 -16.229 1 16.85 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -10.579 -7.767 -17.622 1 17.15 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -11.302 -7.702 -15.241 1 12.93 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -9.879 -5.872 -16.298 1 15.51 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -8.888 -8.16 -15.853 1 14.83 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -8.707 -9.348 -14.813 1 15.97 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -9.489 -10.526 -15.415 1 19.45 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -8.854 -9.068 -13.327 1 13.18 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -7.143 -9.68 -14.96 1 15.81 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -6.629 -9.984 -16.278 1 18.67 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -5.389 -10.896 -16.132 1 19.72 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -4.295 -10.162 -15.514 1 18.49 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -5.664 -12.026 -15.14 1 23.51 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -4.895 -13.158 -15.552 1 23.6 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -5.113 -11.585 -13.767 1 21.98 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -4.613 -12.626 -12.888 1 25.07 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -3.971 -10.71 -14.221 1 20.65 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -3.708 -9.612 -13.315 1 20.04 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -4.619 -8.691 -12.918 1 16.23 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -4.042 -7.811 -12.114 1 17.97 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -2.724 -8.155 -11.996 1 18.12 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -1.567 -7.663 -11.284 1 15.79 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -1.645 -6.592 -10.58 1 13.81 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -0.411 -8.299 -11.451 1 16.34 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -0.264 -9.453 -12.209 1 18.58 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 0.933 -10.072 -12.372 1 22.36 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -1.29 -9.961 -12.892 1 17.5 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -2.529 -9.383 -12.78 1 17.68 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #