data_3SXC # _model_server_result.job_id 9vI-OI5Vlt9c7BQZXCdmhg _model_server_result.datetime_utc '2024-11-30 06:04:43' _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 3sxc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3SXC # _exptl.entry_id 3SXC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 3SXC _cell.length_a 52.55 _cell.length_b 149.88 _cell.length_c 78.81 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SXC _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F 1 1 A,B,C,D,E,F 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 52.55 0 39.405 # _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 B O1A UDP . A UDP 1 1_555 D MN MN . A MN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc2 B O3B UDP . A UDP 1 1_555 D MN MN . A MN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc3 D MN MN . A MN 8 1_555 A OD2 ASP 150 A ASP 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc4 D MN MN . A MN 8 1_555 A OD1 ASP 152 A ASP 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-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 N1 C2 UDP sing 398 n n N1 C6 UDP sing 399 n n N1 C1' UDP sing 400 n n C2 N3 UDP sing 401 n n C2 O2 UDP doub 402 n n N3 C4 UDP sing 403 n n N3 HN3 UDP sing 404 n n C4 C5 UDP sing 405 n n C4 O4 UDP doub 406 n n C5 C6 UDP doub 407 n n C5 H5 UDP sing 408 n n C6 H6 UDP sing 409 n n C1' C2' UDP sing 410 n n C1' O4' UDP sing 411 n n C1' H1' UDP sing 412 n n C2' O2' UDP sing 413 n n C2' C3' UDP sing 414 n n C2' H2' UDP sing 415 n n O2' HO2' UDP sing 416 n n C3' C4' UDP sing 417 n n C3' O3' UDP sing 418 n n C3' H3' UDP sing 419 n n C4' O4' UDP sing 420 n n C4' C5' UDP sing 421 n n C4' H4' UDP sing 422 n n O3' HO3' UDP sing 423 n n C5' O5' UDP sing 424 n n C5' "H5'1" UDP sing 425 n n C5' "H5'2" UDP sing 426 n n O5' PA UDP sing 427 n n PA O1A UDP doub 428 n n PA O2A UDP sing 429 n n PA O3A UDP sing 430 n n O2A HOA2 UDP sing 431 n n O3A PB UDP sing 432 n n PB O1B UDP doub 433 n n PB O2B UDP sing 434 n n PB O3B UDP sing 435 n n O2B HOB2 UDP sing 436 n n O3B HOB3 UDP sing 437 n n # _atom_sites.entry_id 3SXC _atom_sites.fract_transf_matrix[1][1] 0.019029 _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] 0.006672 _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] 0.012689 _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 UDP A 1 1 1 UDP UDP . C 3 GAL A 1 2 2 GAL GAL . D 4 MN A 1 8 8 MN MN . E 5 PEG A 1 9 9 PEG PEG . F 6 HOH A 1 3 3 HOH HOH . F 6 HOH A 2 4 4 HOH HOH . F 6 HOH A 3 5 5 HOH HOH . F 6 HOH A 4 6 6 HOH HOH . F 6 HOH A 5 7 7 HOH HOH . F 6 HOH A 6 10 10 HOH HOH . F 6 HOH A 7 11 11 HOH HOH . F 6 HOH A 8 12 12 HOH HOH . F 6 HOH A 9 13 13 HOH HOH . F 6 HOH A 10 14 14 HOH HOH . F 6 HOH A 11 15 15 HOH HOH . F 6 HOH A 12 16 16 HOH HOH . F 6 HOH A 13 17 17 HOH HOH . F 6 HOH A 14 18 18 HOH HOH . F 6 HOH A 15 19 19 HOH HOH . F 6 HOH A 16 20 20 HOH HOH . F 6 HOH A 17 21 21 HOH HOH . F 6 HOH A 18 22 22 HOH HOH . F 6 HOH A 19 23 23 HOH HOH . F 6 HOH A 20 24 24 HOH HOH . F 6 HOH A 21 25 25 HOH HOH . F 6 HOH A 22 26 26 HOH HOH . F 6 HOH A 23 27 27 HOH HOH . F 6 HOH A 24 28 28 HOH HOH . F 6 HOH A 25 29 29 HOH HOH . F 6 HOH A 26 30 30 HOH HOH . F 6 HOH A 27 31 31 HOH HOH . F 6 HOH A 28 32 32 HOH HOH . F 6 HOH A 29 33 33 HOH HOH . F 6 HOH A 30 34 34 HOH HOH . F 6 HOH A 31 35 35 HOH HOH . F 6 HOH A 32 36 36 HOH HOH . F 6 HOH A 33 37 37 HOH HOH . F 6 HOH A 34 38 38 HOH HOH . F 6 HOH A 35 39 39 HOH HOH . F 6 HOH A 36 40 40 HOH HOH . F 6 HOH A 37 41 41 HOH HOH . F 6 HOH A 38 42 42 HOH HOH . F 6 HOH A 39 43 43 HOH HOH . F 6 HOH A 40 44 44 HOH HOH . F 6 HOH A 41 45 45 HOH HOH . F 6 HOH A 42 46 46 HOH HOH . F 6 HOH A 43 47 47 HOH HOH . F 6 HOH A 44 48 48 HOH HOH . F 6 HOH A 45 49 49 HOH HOH . F 6 HOH A 46 50 50 HOH HOH . F 6 HOH A 47 51 51 HOH HOH . F 6 HOH A 48 52 52 HOH HOH . F 6 HOH A 49 53 53 HOH HOH . F 6 HOH A 50 54 54 HOH HOH . F 6 HOH A 51 55 55 HOH HOH . F 6 HOH A 52 56 56 HOH HOH . F 6 HOH A 53 57 57 HOH HOH . F 6 HOH A 54 58 58 HOH HOH . F 6 HOH A 55 59 59 HOH HOH . F 6 HOH A 56 60 60 HOH HOH . F 6 HOH A 57 61 61 HOH HOH . F 6 HOH A 58 355 1 HOH HOH . F 6 HOH A 59 356 2 HOH HOH . F 6 HOH A 60 357 8 HOH HOH . F 6 HOH A 61 358 9 HOH HOH . F 6 HOH A 62 359 62 HOH HOH . F 6 HOH A 63 360 63 HOH HOH . F 6 HOH A 64 361 64 HOH HOH . F 6 HOH A 65 362 65 HOH HOH . F 6 HOH A 66 363 66 HOH HOH . F 6 HOH A 67 364 67 HOH HOH . F 6 HOH A 68 365 68 HOH HOH . F 6 HOH A 69 366 69 HOH HOH . F 6 HOH A 70 367 70 HOH HOH . F 6 HOH A 71 368 71 HOH HOH . F 6 HOH A 72 369 72 HOH HOH . F 6 HOH A 73 370 73 HOH HOH . F 6 HOH A 74 371 74 HOH HOH . F 6 HOH A 75 372 75 HOH HOH . F 6 HOH A 76 373 76 HOH HOH . F 6 HOH A 77 374 77 HOH HOH . F 6 HOH A 78 375 78 HOH HOH . F 6 HOH A 79 376 79 HOH HOH . F 6 HOH A 80 377 80 HOH HOH . F 6 HOH A 81 378 81 HOH HOH . F 6 HOH A 82 379 82 HOH HOH . F 6 HOH A 83 380 83 HOH HOH . F 6 HOH A 84 381 84 HOH HOH . F 6 HOH A 85 382 85 HOH HOH . F 6 HOH A 86 383 86 HOH HOH . F 6 HOH A 87 384 87 HOH HOH . F 6 HOH A 88 385 88 HOH HOH . F 6 HOH A 89 386 89 HOH HOH . F 6 HOH A 90 387 90 HOH HOH . F 6 HOH A 91 388 91 HOH HOH . F 6 HOH A 92 389 92 HOH HOH . F 6 HOH A 93 390 93 HOH HOH . F 6 HOH A 94 391 94 HOH HOH . F 6 HOH A 95 392 95 HOH HOH . F 6 HOH A 96 393 96 HOH HOH . F 6 HOH A 97 394 97 HOH HOH . F 6 HOH A 98 395 98 HOH HOH . F 6 HOH A 99 396 99 HOH HOH . F 6 HOH A 100 397 100 HOH HOH . F 6 HOH A 101 398 101 HOH HOH . F 6 HOH A 102 399 102 HOH HOH . F 6 HOH A 103 400 103 HOH HOH . F 6 HOH A 104 401 104 HOH HOH . F 6 HOH A 105 402 105 HOH HOH . F 6 HOH A 106 403 106 HOH HOH . F 6 HOH A 107 404 107 HOH HOH . F 6 HOH A 108 405 108 HOH HOH . F 6 HOH A 109 406 109 HOH HOH . F 6 HOH A 110 407 110 HOH HOH . F 6 HOH A 111 408 111 HOH HOH . F 6 HOH A 112 409 112 HOH HOH . F 6 HOH A 113 410 113 HOH HOH . F 6 HOH A 114 411 114 HOH HOH . F 6 HOH A 115 412 115 HOH HOH . F 6 HOH A 116 413 116 HOH HOH . F 6 HOH A 117 414 117 HOH HOH . F 6 HOH A 118 415 118 HOH HOH . F 6 HOH A 119 416 119 HOH HOH . F 6 HOH A 120 417 120 HOH HOH . F 6 HOH A 121 418 121 HOH HOH . F 6 HOH A 122 419 122 HOH HOH . F 6 HOH A 123 420 123 HOH HOH . F 6 HOH A 124 421 124 HOH HOH . F 6 HOH A 125 422 125 HOH HOH . F 6 HOH A 126 423 126 HOH HOH . F 6 HOH A 127 424 127 HOH HOH . F 6 HOH A 128 425 128 HOH HOH . F 6 HOH A 129 426 129 HOH HOH . F 6 HOH A 130 427 130 HOH HOH . F 6 HOH A 131 428 131 HOH HOH . F 6 HOH A 132 429 132 HOH HOH . F 6 HOH A 133 430 133 HOH HOH . F 6 HOH A 134 431 134 HOH HOH . F 6 HOH A 135 432 135 HOH HOH . F 6 HOH A 136 433 136 HOH HOH . F 6 HOH A 137 434 137 HOH HOH . F 6 HOH A 138 435 138 HOH HOH . F 6 HOH A 139 436 139 HOH HOH . F 6 HOH A 140 437 140 HOH HOH . F 6 HOH A 141 438 141 HOH HOH . F 6 HOH A 142 439 142 HOH HOH . F 6 HOH A 143 440 143 HOH HOH . F 6 HOH A 144 441 144 HOH HOH . F 6 HOH A 145 442 145 HOH HOH . F 6 HOH A 146 443 146 HOH HOH . F 6 HOH A 147 444 147 HOH HOH . F 6 HOH A 148 445 148 HOH HOH . F 6 HOH A 149 446 149 HOH HOH . F 6 HOH A 150 447 150 HOH HOH . F 6 HOH A 151 448 151 HOH HOH . F 6 HOH A 152 449 152 HOH HOH . F 6 HOH A 153 450 153 HOH HOH . F 6 HOH A 154 451 154 HOH HOH . F 6 HOH A 155 452 155 HOH HOH . F 6 HOH A 156 453 156 HOH HOH . F 6 HOH A 157 454 157 HOH HOH . F 6 HOH A 158 455 158 HOH HOH . F 6 HOH A 159 456 159 HOH HOH . F 6 HOH A 160 457 160 HOH HOH . F 6 HOH A 161 458 161 HOH HOH . F 6 HOH A 162 459 162 HOH HOH . F 6 HOH A 163 460 163 HOH HOH . F 6 HOH A 164 461 164 HOH HOH . F 6 HOH A 165 462 165 HOH HOH . F 6 HOH A 166 463 166 HOH HOH . F 6 HOH A 167 464 167 HOH HOH . F 6 HOH A 168 465 168 HOH HOH . F 6 HOH A 169 466 169 HOH HOH . F 6 HOH A 170 467 170 HOH HOH . F 6 HOH A 171 468 171 HOH HOH . F 6 HOH A 172 469 172 HOH HOH . F 6 HOH A 173 470 173 HOH HOH . F 6 HOH A 174 471 174 HOH HOH . F 6 HOH A 175 472 175 HOH HOH . F 6 HOH A 176 473 176 HOH HOH . F 6 HOH A 177 474 177 HOH HOH . F 6 HOH A 178 475 178 HOH HOH . F 6 HOH A 179 476 179 HOH HOH . F 6 HOH A 180 477 180 HOH HOH . F 6 HOH A 181 478 181 HOH HOH . F 6 HOH A 182 479 182 HOH HOH . F 6 HOH A 183 480 183 HOH HOH . F 6 HOH A 184 481 184 HOH HOH . F 6 HOH A 185 482 185 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 N N1 UDP . . . B 2 9.93 23.373 -7.885 1 43.43 ? N1 UDP 1 A 1 HETATM 2 C C2 UDP . . . B 2 8.739 24.076 -8.113 1 44.06 ? C2 UDP 1 A 1 HETATM 3 N N3 UDP . . . B 2 8.209 24.055 -9.468 1 46.93 ? N3 UDP 1 A 1 HETATM 4 C C4 UDP . . . B 2 8.892 23.347 -10.544 1 51 ? C4 UDP 1 A 1 HETATM 5 C C5 UDP . . . B 2 10.086 22.657 -10.275 1 49.25 ? C5 UDP 1 A 1 HETATM 6 C C6 UDP . . . B 2 10.586 22.676 -8.955 1 47.96 ? C6 UDP 1 A 1 HETATM 7 O O2 UDP . . . B 2 8.197 24.678 -7.155 1 30.03 ? O2 UDP 1 A 1 HETATM 8 O O4 UDP . . . B 2 8.414 23.328 -11.685 1 52.25 ? O4 UDP 1 A 1 HETATM 9 C C1' UDP . . . B 2 10.449 23.404 -6.505 1 43.49 ? C1' UDP 1 A 1 HETATM 10 C C2' UDP . . . B 2 9.501 22.583 -5.593 1 39.9 ? C2' UDP 1 A 1 HETATM 11 O O2' UDP . . . B 2 9.581 22.989 -4.239 1 35.72 ? O2' UDP 1 A 1 HETATM 12 C C3' UDP . . . B 2 10.177 21.238 -5.646 1 38.88 ? C3' UDP 1 A 1 HETATM 13 C C4' UDP . . . B 2 11.671 21.631 -5.623 1 39.03 ? C4' UDP 1 A 1 HETATM 14 O O4' UDP . . . B 2 11.735 22.722 -6.536 1 44.7 ? O4' UDP 1 A 1 HETATM 15 O O3' UDP . . . B 2 9.821 20.613 -4.428 1 36.13 ? O3' UDP 1 A 1 HETATM 16 C C5' UDP . . . B 2 12.747 20.624 -6.113 1 32.64 ? C5' UDP 1 A 1 HETATM 17 O O5' UDP . . . B 2 12.461 20.118 -7.378 0.4 28.95 ? O5' UDP 1 A 1 HETATM 18 P PA UDP . . . B 2 11.731 18.715 -7.509 0.4 28.09 ? PA UDP 1 A 1 HETATM 19 O O1A UDP . . . B 2 11.017 18.381 -6.226 0.4 25.91 ? O1A UDP 1 A 1 HETATM 20 O O2A UDP . . . B 2 11.01 18.748 -8.766 0.4 30.52 ? O2A UDP 1 A 1 HETATM 21 O O3A UDP . . . B 2 13.015 17.771 -7.69 0.4 28.34 ? O3A UDP 1 A 1 HETATM 22 P PB UDP . . . B 2 13.123 16.271 -7.082 0.4 29.8 ? PB UDP 1 A 1 HETATM 23 O O1B UDP . . . B 2 12.098 15.32 -7.898 0.4 30.03 ? O1B UDP 1 A 1 HETATM 24 O O2B UDP . . . B 2 14.575 15.743 -7.496 0.4 27.36 ? O2B UDP 1 A 1 HETATM 25 O O3B UDP . . . B 2 12.901 16.178 -5.644 0.4 25.69 ? O3B UDP 1 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #