data_3I0K # _model_server_result.job_id Rh-JFnNfsA5OaPOuaLU4Lg _model_server_result.datetime_utc '2024-10-30 01:28:29' _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 3i0k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1}' # _entry.id 3I0K # _exptl.entry_id 3I0K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _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 3I0K _cell.length_a 52.104 _cell.length_b 150.41 _cell.length_c 79.253 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3I0K _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 39.6265 # _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 # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 FUC _pdbx_entity_branch_link.comp_id_2 BHG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B BHG 1 B 1 BHG A 400 BHG 2 n B FUC 2 B 2 FUC A 356 FUC # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id O2 _struct_conn.ptnr1_label_comp_id BHG _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id BHG _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C1 _struct_conn.ptnr2_label_comp_id FUC _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id FUC _struct_conn.ptnr2_auth_seq_id 2 _struct_conn.ptnr2_symmetry 1_555 _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 1.461 _struct_conn.pdbx_value_order ? # _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 423 n n N1 C6 UDP sing 424 n n N1 C1' UDP sing 425 n n C2 N3 UDP sing 426 n n C2 O2 UDP doub 427 n n N3 C4 UDP sing 428 n n N3 HN3 UDP sing 429 n n C4 C5 UDP sing 430 n n C4 O4 UDP doub 431 n n C5 C6 UDP doub 432 n n C5 H5 UDP sing 433 n n C6 H6 UDP sing 434 n n C1' C2' UDP sing 435 n n C1' O4' UDP sing 436 n n C1' H1' UDP sing 437 n n C2' O2' UDP sing 438 n n C2' C3' UDP sing 439 n n C2' H2' UDP sing 440 n n O2' HO2' UDP sing 441 n n C3' C4' UDP sing 442 n n C3' O3' UDP sing 443 n n C3' H3' UDP sing 444 n n C4' O4' UDP sing 445 n n C4' C5' UDP sing 446 n n C4' H4' UDP sing 447 n n O3' HO3' UDP sing 448 n n C5' O5' UDP sing 449 n n C5' "H5'1" UDP sing 450 n n C5' "H5'2" UDP sing 451 n n O5' PA UDP sing 452 n n PA O1A UDP doub 453 n n PA O2A UDP sing 454 n n PA O3A UDP sing 455 n n O2A HOA2 UDP sing 456 n n O3A PB UDP sing 457 n n PB O1B UDP doub 458 n n PB O2B UDP sing 459 n n PB O3B UDP sing 460 n n O2B HOB2 UDP sing 461 n n O3B HOB3 UDP sing 462 n n # _atom_sites.entry_id 3I0K _atom_sites.fract_transf_matrix[1][1] 0.019192 _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] 0.006648 _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] 0.012618 _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 UDP A 1 1 1 UDP UDP . D 4 HOH A 1 2 2 HOH HOH . D 4 HOH A 2 3 3 HOH HOH . D 4 HOH A 3 4 4 HOH HOH . D 4 HOH A 4 5 5 HOH HOH . D 4 HOH A 5 6 6 HOH HOH . D 4 HOH A 6 7 7 HOH HOH . D 4 HOH A 7 8 8 HOH HOH . D 4 HOH A 8 9 9 HOH HOH . D 4 HOH A 9 10 10 HOH HOH . D 4 HOH A 10 11 11 HOH HOH . D 4 HOH A 11 12 12 HOH HOH . D 4 HOH A 12 13 13 HOH HOH . D 4 HOH A 13 14 14 HOH HOH . D 4 HOH A 14 15 15 HOH HOH . D 4 HOH A 15 16 16 HOH HOH . D 4 HOH A 16 17 17 HOH HOH . D 4 HOH A 17 18 18 HOH HOH . D 4 HOH A 18 19 19 HOH HOH . D 4 HOH A 19 20 20 HOH HOH . D 4 HOH A 20 21 21 HOH HOH . D 4 HOH A 21 22 22 HOH HOH . D 4 HOH A 22 23 23 HOH HOH . D 4 HOH A 23 24 24 HOH HOH . D 4 HOH A 24 25 25 HOH HOH . D 4 HOH A 25 26 26 HOH HOH . D 4 HOH A 26 27 27 HOH HOH . D 4 HOH A 27 28 28 HOH HOH . D 4 HOH A 28 29 29 HOH HOH . D 4 HOH A 29 30 30 HOH HOH . D 4 HOH A 30 31 31 HOH HOH . D 4 HOH A 31 32 32 HOH HOH . D 4 HOH A 32 33 33 HOH HOH . D 4 HOH A 33 34 34 HOH HOH . D 4 HOH A 34 35 35 HOH HOH . D 4 HOH A 35 36 36 HOH HOH . D 4 HOH A 36 37 37 HOH HOH . D 4 HOH A 37 38 38 HOH HOH . D 4 HOH A 38 39 39 HOH HOH . D 4 HOH A 39 40 40 HOH HOH . D 4 HOH A 40 41 41 HOH HOH . D 4 HOH A 41 42 42 HOH HOH . D 4 HOH A 42 43 43 HOH HOH . D 4 HOH A 43 44 44 HOH HOH . D 4 HOH A 44 45 45 HOH HOH . D 4 HOH A 45 46 46 HOH HOH . D 4 HOH A 46 47 47 HOH HOH . D 4 HOH A 47 48 48 HOH HOH . D 4 HOH A 48 49 49 HOH HOH . D 4 HOH A 49 50 50 HOH HOH . D 4 HOH A 50 51 51 HOH HOH . D 4 HOH A 51 52 52 HOH HOH . D 4 HOH A 52 53 53 HOH HOH . D 4 HOH A 53 54 54 HOH HOH . D 4 HOH A 54 55 55 HOH HOH . D 4 HOH A 55 56 56 HOH HOH . D 4 HOH A 56 57 57 HOH HOH . D 4 HOH A 57 58 58 HOH HOH . D 4 HOH A 58 59 59 HOH HOH . D 4 HOH A 59 60 60 HOH HOH . D 4 HOH A 60 61 61 HOH HOH . D 4 HOH A 61 62 62 HOH HOH . D 4 HOH A 62 63 63 HOH HOH . D 4 HOH A 63 64 64 HOH HOH . D 4 HOH A 64 65 65 HOH HOH . D 4 HOH A 65 66 66 HOH HOH . D 4 HOH A 66 67 67 HOH HOH . D 4 HOH A 67 68 68 HOH HOH . D 4 HOH A 68 357 69 HOH HOH . D 4 HOH A 69 358 70 HOH HOH . D 4 HOH A 70 359 71 HOH HOH . D 4 HOH A 71 360 72 HOH HOH . D 4 HOH A 72 361 73 HOH HOH . D 4 HOH A 73 362 74 HOH HOH . D 4 HOH A 74 363 75 HOH HOH . D 4 HOH A 75 364 76 HOH HOH . D 4 HOH A 76 365 77 HOH HOH . D 4 HOH A 77 366 78 HOH HOH . D 4 HOH A 78 367 79 HOH HOH . D 4 HOH A 79 368 80 HOH HOH . D 4 HOH A 80 369 81 HOH HOH . D 4 HOH A 81 370 82 HOH HOH . D 4 HOH A 82 371 83 HOH HOH . D 4 HOH A 83 372 84 HOH HOH . D 4 HOH A 84 373 85 HOH HOH . D 4 HOH A 85 374 86 HOH HOH . D 4 HOH A 86 375 87 HOH HOH . D 4 HOH A 87 376 88 HOH HOH . D 4 HOH A 88 377 89 HOH HOH . D 4 HOH A 89 378 90 HOH HOH . D 4 HOH A 90 379 91 HOH HOH . D 4 HOH A 91 380 92 HOH HOH . D 4 HOH A 92 381 93 HOH HOH . D 4 HOH A 93 382 94 HOH HOH . D 4 HOH A 94 383 95 HOH HOH . D 4 HOH A 95 384 96 HOH HOH . D 4 HOH A 96 385 97 HOH HOH . D 4 HOH A 97 386 98 HOH HOH . D 4 HOH A 98 387 99 HOH HOH . D 4 HOH A 99 388 100 HOH HOH . D 4 HOH A 100 389 101 HOH HOH . D 4 HOH A 101 390 102 HOH HOH . D 4 HOH A 102 391 103 HOH HOH . D 4 HOH A 103 392 104 HOH HOH . D 4 HOH A 104 393 105 HOH HOH . D 4 HOH A 105 394 106 HOH HOH . D 4 HOH A 106 395 107 HOH HOH . D 4 HOH A 107 396 108 HOH HOH . D 4 HOH A 108 397 109 HOH HOH . D 4 HOH A 109 398 110 HOH HOH . D 4 HOH A 110 399 111 HOH HOH . D 4 HOH A 111 401 112 HOH HOH . D 4 HOH A 112 402 113 HOH HOH . D 4 HOH A 113 403 114 HOH HOH . D 4 HOH A 114 404 115 HOH HOH . D 4 HOH A 115 405 116 HOH HOH . D 4 HOH A 116 406 117 HOH HOH . D 4 HOH A 117 407 118 HOH HOH . D 4 HOH A 118 408 119 HOH HOH . D 4 HOH A 119 409 120 HOH HOH . D 4 HOH A 120 410 121 HOH HOH . D 4 HOH A 121 411 122 HOH HOH . D 4 HOH A 122 412 123 HOH HOH . D 4 HOH A 123 413 124 HOH HOH . D 4 HOH A 124 414 125 HOH HOH . D 4 HOH A 125 415 126 HOH HOH . D 4 HOH A 126 416 127 HOH HOH . D 4 HOH A 127 417 128 HOH HOH . D 4 HOH A 128 418 129 HOH HOH . D 4 HOH A 129 419 130 HOH HOH . D 4 HOH A 130 420 131 HOH HOH . D 4 HOH A 131 421 132 HOH HOH . D 4 HOH A 132 422 133 HOH HOH . D 4 HOH A 133 423 134 HOH HOH . D 4 HOH A 134 424 135 HOH HOH . D 4 HOH A 135 425 136 HOH HOH . D 4 HOH A 136 426 137 HOH HOH . D 4 HOH A 137 427 138 HOH HOH . D 4 HOH A 138 428 139 HOH HOH . D 4 HOH A 139 429 140 HOH HOH . D 4 HOH A 140 430 141 HOH HOH . D 4 HOH A 141 431 142 HOH HOH . D 4 HOH A 142 432 143 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 . . . C 3 -16.203 23.46 -7.817 1 57.47 ? N1 UDP 1 A 1 HETATM 2 C C2 UDP . . . C 3 -17.383 24.154 -8.111 1 55.98 ? C2 UDP 1 A 1 HETATM 3 N N3 UDP . . . C 3 -17.8 24.204 -9.485 1 58.94 ? N3 UDP 1 A 1 HETATM 4 C C4 UDP . . . C 3 -17.031 23.578 -10.549 1 61.24 ? C4 UDP 1 A 1 HETATM 5 C C5 UDP . . . C 3 -15.846 22.905 -10.213 1 61.16 ? C5 UDP 1 A 1 HETATM 6 C C6 UDP . . . C 3 -15.452 22.843 -8.87 1 59.98 ? C6 UDP 1 A 1 HETATM 7 O O2 UDP . . . C 3 -18.021 24.677 -7.191 1 48.33 ? O2 UDP 1 A 1 HETATM 8 O O4 UDP . . . C 3 -17.383 23.626 -11.743 1 59.72 ? O4 UDP 1 A 1 HETATM 9 C C1' UDP . . . C 3 -15.743 23.395 -6.397 1 57.26 ? C1' UDP 1 A 1 HETATM 10 C C2' UDP . . . C 3 -16.657 22.458 -5.642 1 54.17 ? C2' UDP 1 A 1 HETATM 11 O O2' UDP . . . C 3 -16.612 22.807 -4.279 1 49.04 ? O2' UDP 1 A 1 HETATM 12 C C3' UDP . . . C 3 -15.94 21.155 -5.805 1 56.55 ? C3' UDP 1 A 1 HETATM 13 C C4' UDP . . . C 3 -14.447 21.506 -5.65 1 58.35 ? C4' UDP 1 A 1 HETATM 14 O O4' UDP . . . C 3 -14.35 22.885 -6.192 1 60.4 ? O4' UDP 1 A 1 HETATM 15 O O3' UDP . . . C 3 -16.322 20.388 -4.686 1 61.49 ? O3' UDP 1 A 1 HETATM 16 C C5' UDP . . . C 3 -13.34 20.473 -6.141 1 58.74 ? C5' UDP 1 A 1 HETATM 17 O O5' UDP . . . C 3 -13.649 19.665 -7.32 1 62.98 ? O5' UDP 1 A 1 HETATM 18 P PA UDP . . . C 3 -14.534 18.188 -7.445 1 66.65 ? PA UDP 1 A 1 HETATM 19 O O1A UDP . . . C 3 -14.917 19.123 -8.756 1 67.46 ? O1A UDP 1 A 1 HETATM 20 O O2A UDP . . . C 3 -15.195 18.439 -6.097 1 65.67 ? O2A UDP 1 A 1 HETATM 21 O O3A UDP . . . C 3 -12.983 17.438 -7.424 1 65.75 ? O3A UDP 1 A 1 HETATM 22 P PB UDP . . . C 3 -12.592 15.911 -6.754 1 66.3 ? PB UDP 1 A 1 HETATM 23 O O1B UDP . . . C 3 -11.182 16.234 -7.583 1 66.06 ? O1B UDP 1 A 1 HETATM 24 O O2B UDP . . . C 3 -13.761 15.265 -7.491 1 65.25 ? O2B UDP 1 A 1 HETATM 25 O O3B UDP . . . C 3 -12.807 16.734 -5.334 1 66.74 ? O3B UDP 1 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 25 #