data_7UFP # _model_server_result.job_id vb_HSiL0V-cdZwyy7lPyDA _model_server_result.datetime_utc '2025-02-26 15:03:54' _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 7ufp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7UFP # _exptl.entry_id 7UFP _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 98.19 _cell.angle_gamma 90 _cell.entry_id 7UFP _cell.length_a 126.763 _cell.length_b 44.975 _cell.length_c 98.046 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7UFP _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _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,H _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 # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 338 _struct_conn.ptnr1_auth_asym_id I _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 330 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 483 _struct_conn.ptnr2_auth_asym_id I _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 475 _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 2.037 _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 362 n n N1 C6 UDP sing 363 n n N1 C1' UDP sing 364 n n C2 N3 UDP sing 365 n n C2 O2 UDP doub 366 n n N3 C4 UDP sing 367 n n N3 HN3 UDP sing 368 n n C4 C5 UDP sing 369 n n C4 O4 UDP doub 370 n n C5 C6 UDP doub 371 n n C5 H5 UDP sing 372 n n C6 H6 UDP sing 373 n n C1' C2' UDP sing 374 n n C1' O4' UDP sing 375 n n C1' H1' UDP sing 376 n n C2' O2' UDP sing 377 n n C2' C3' UDP sing 378 n n C2' H2' UDP sing 379 n n O2' HO2' UDP sing 380 n n C3' C4' UDP sing 381 n n C3' O3' UDP sing 382 n n C3' H3' UDP sing 383 n n C4' O4' UDP sing 384 n n C4' C5' UDP sing 385 n n C4' H4' UDP sing 386 n n O3' HO3' UDP sing 387 n n C5' O5' UDP sing 388 n n C5' "H5'1" UDP sing 389 n n C5' "H5'2" UDP sing 390 n n O5' PA UDP sing 391 n n PA O1A UDP doub 392 n n PA O2A UDP sing 393 n n PA O3A UDP sing 394 n n O2A HOA2 UDP sing 395 n n O3A PB UDP sing 396 n n PB O1B UDP doub 397 n n PB O2B UDP sing 398 n n PB O3B UDP sing 399 n n O2B HOB2 UDP sing 400 n n O3B HOB3 UDP sing 401 n n # _atom_sites.entry_id 7UFP _atom_sites.fract_transf_matrix[1][1] 0.007889 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001135 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022235 _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] 0.010304 _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 I 1 501 501 UDP UDP . C 3 SO4 I 1 502 1 SO4 SO4 . D 3 SO4 I 1 503 2 SO4 SO4 . E 3 SO4 I 1 504 3 SO4 SO4 . F 3 SO4 I 1 505 4 SO4 SO4 . G 3 SO4 I 1 506 5 SO4 SO4 . H 4 HOH I 1 601 295 HOH HOH . H 4 HOH I 2 602 282 HOH HOH . H 4 HOH I 3 603 156 HOH HOH . H 4 HOH I 4 604 12 HOH HOH . H 4 HOH I 5 605 15 HOH HOH . H 4 HOH I 6 606 123 HOH HOH . H 4 HOH I 7 607 31 HOH HOH . H 4 HOH I 8 608 96 HOH HOH . H 4 HOH I 9 609 2 HOH HOH . H 4 HOH I 10 610 71 HOH HOH . H 4 HOH I 11 611 195 HOH HOH . H 4 HOH I 12 612 59 HOH HOH . H 4 HOH I 13 613 28 HOH HOH . H 4 HOH I 14 614 297 HOH HOH . H 4 HOH I 15 615 127 HOH HOH . H 4 HOH I 16 616 214 HOH HOH . H 4 HOH I 17 617 94 HOH HOH . H 4 HOH I 18 618 39 HOH HOH . H 4 HOH I 19 619 168 HOH HOH . H 4 HOH I 20 620 1 HOH HOH . H 4 HOH I 21 621 142 HOH HOH . H 4 HOH I 22 622 136 HOH HOH . H 4 HOH I 23 623 239 HOH HOH . H 4 HOH I 24 624 83 HOH HOH . H 4 HOH I 25 625 135 HOH HOH . H 4 HOH I 26 626 90 HOH HOH . H 4 HOH I 27 627 312 HOH HOH . H 4 HOH I 28 628 9 HOH HOH . H 4 HOH I 29 629 13 HOH HOH . H 4 HOH I 30 630 20 HOH HOH . H 4 HOH I 31 631 144 HOH HOH . H 4 HOH I 32 632 32 HOH HOH . H 4 HOH I 33 633 299 HOH HOH . H 4 HOH I 34 634 60 HOH HOH . H 4 HOH I 35 635 68 HOH HOH . H 4 HOH I 36 636 134 HOH HOH . H 4 HOH I 37 637 106 HOH HOH . H 4 HOH I 38 638 277 HOH HOH . H 4 HOH I 39 639 66 HOH HOH . H 4 HOH I 40 640 65 HOH HOH . H 4 HOH I 41 641 53 HOH HOH . H 4 HOH I 42 642 43 HOH HOH . H 4 HOH I 43 643 38 HOH HOH . H 4 HOH I 44 644 273 HOH HOH . H 4 HOH I 45 645 222 HOH HOH . H 4 HOH I 46 646 40 HOH HOH . H 4 HOH I 47 647 199 HOH HOH . H 4 HOH I 48 648 55 HOH HOH . H 4 HOH I 49 649 52 HOH HOH . H 4 HOH I 50 650 87 HOH HOH . H 4 HOH I 51 651 50 HOH HOH . H 4 HOH I 52 652 114 HOH HOH . H 4 HOH I 53 653 147 HOH HOH . H 4 HOH I 54 654 36 HOH HOH . H 4 HOH I 55 655 116 HOH HOH . H 4 HOH I 56 656 10 HOH HOH . H 4 HOH I 57 657 25 HOH HOH . H 4 HOH I 58 658 279 HOH HOH . H 4 HOH I 59 659 18 HOH HOH . H 4 HOH I 60 660 189 HOH HOH . H 4 HOH I 61 661 118 HOH HOH . H 4 HOH I 62 662 22 HOH HOH . H 4 HOH I 63 663 292 HOH HOH . H 4 HOH I 64 664 4 HOH HOH . H 4 HOH I 65 665 284 HOH HOH . H 4 HOH I 66 666 16 HOH HOH . H 4 HOH I 67 667 33 HOH HOH . H 4 HOH I 68 668 70 HOH HOH . H 4 HOH I 69 669 45 HOH HOH . H 4 HOH I 70 670 81 HOH HOH . H 4 HOH I 71 671 188 HOH HOH . H 4 HOH I 72 672 46 HOH HOH . H 4 HOH I 73 673 86 HOH HOH . H 4 HOH I 74 674 27 HOH HOH . H 4 HOH I 75 675 74 HOH HOH . H 4 HOH I 76 676 62 HOH HOH . H 4 HOH I 77 677 315 HOH HOH . H 4 HOH I 78 678 35 HOH HOH . H 4 HOH I 79 679 17 HOH HOH . H 4 HOH I 80 680 73 HOH HOH . H 4 HOH I 81 681 303 HOH HOH . H 4 HOH I 82 682 48 HOH HOH . H 4 HOH I 83 683 192 HOH HOH . H 4 HOH I 84 684 92 HOH HOH . H 4 HOH I 85 685 162 HOH HOH . H 4 HOH I 86 686 79 HOH HOH . H 4 HOH I 87 687 97 HOH HOH . H 4 HOH I 88 688 23 HOH HOH . H 4 HOH I 89 689 167 HOH HOH . H 4 HOH I 90 690 58 HOH HOH . H 4 HOH I 91 691 105 HOH HOH . H 4 HOH I 92 692 151 HOH HOH . H 4 HOH I 93 693 3 HOH HOH . H 4 HOH I 94 694 30 HOH HOH . H 4 HOH I 95 695 203 HOH HOH . H 4 HOH I 96 696 193 HOH HOH . H 4 HOH I 97 697 34 HOH HOH . H 4 HOH I 98 698 24 HOH HOH . H 4 HOH I 99 699 125 HOH HOH . H 4 HOH I 100 700 115 HOH HOH . H 4 HOH I 101 701 314 HOH HOH . H 4 HOH I 102 702 84 HOH HOH . H 4 HOH I 103 703 42 HOH HOH . H 4 HOH I 104 704 285 HOH HOH . H 4 HOH I 105 705 41 HOH HOH . H 4 HOH I 106 706 37 HOH HOH . H 4 HOH I 107 707 88 HOH HOH . H 4 HOH I 108 708 129 HOH HOH . H 4 HOH I 109 709 6 HOH HOH . H 4 HOH I 110 710 304 HOH HOH . H 4 HOH I 111 711 110 HOH HOH . H 4 HOH I 112 712 51 HOH HOH . H 4 HOH I 113 713 14 HOH HOH . H 4 HOH I 114 714 11 HOH HOH . H 4 HOH I 115 715 7 HOH HOH . H 4 HOH I 116 716 296 HOH HOH . H 4 HOH I 117 717 47 HOH HOH . H 4 HOH I 118 718 26 HOH HOH . H 4 HOH I 119 719 91 HOH HOH . H 4 HOH I 120 720 78 HOH HOH . H 4 HOH I 121 721 301 HOH HOH . H 4 HOH I 122 722 61 HOH HOH . H 4 HOH I 123 723 150 HOH HOH . H 4 HOH I 124 724 108 HOH HOH . H 4 HOH I 125 725 75 HOH HOH . H 4 HOH I 126 726 100 HOH HOH . H 4 HOH I 127 727 19 HOH HOH . H 4 HOH I 128 728 21 HOH HOH . H 4 HOH I 129 729 8 HOH HOH . H 4 HOH I 130 730 104 HOH HOH . H 4 HOH I 131 731 191 HOH HOH . H 4 HOH I 132 732 77 HOH HOH . H 4 HOH I 133 733 141 HOH HOH . H 4 HOH I 134 734 120 HOH HOH . H 4 HOH I 135 735 169 HOH HOH . H 4 HOH I 136 736 216 HOH HOH . H 4 HOH I 137 737 289 HOH HOH . H 4 HOH I 138 738 44 HOH HOH . H 4 HOH I 139 739 67 HOH HOH . H 4 HOH I 140 740 5 HOH HOH . H 4 HOH I 141 741 99 HOH HOH . H 4 HOH I 142 742 72 HOH HOH . H 4 HOH I 143 743 306 HOH HOH . H 4 HOH I 144 744 95 HOH HOH . H 4 HOH I 145 745 280 HOH HOH . H 4 HOH I 146 746 103 HOH HOH . H 4 HOH I 147 747 294 HOH HOH . H 4 HOH I 148 748 302 HOH HOH . H 4 HOH I 149 749 54 HOH HOH . H 4 HOH I 150 750 80 HOH HOH . H 4 HOH I 151 751 184 HOH HOH . H 4 HOH I 152 752 82 HOH HOH . H 4 HOH I 153 753 57 HOH HOH . H 4 HOH I 154 754 85 HOH HOH . H 4 HOH I 155 755 310 HOH HOH . H 4 HOH I 156 756 305 HOH HOH . H 4 HOH I 157 757 309 HOH HOH . H 4 HOH I 158 758 76 HOH HOH . H 4 HOH I 159 759 300 HOH HOH . H 4 HOH I 160 760 281 HOH HOH . H 4 HOH I 161 761 69 HOH HOH . H 4 HOH I 162 762 278 HOH HOH . H 4 HOH I 163 763 293 HOH HOH . H 4 HOH I 164 764 283 HOH HOH . H 4 HOH I 165 765 291 HOH HOH . H 4 HOH I 166 766 288 HOH HOH . H 4 HOH I 167 767 140 HOH HOH . H 4 HOH I 168 768 274 HOH HOH . H 4 HOH I 169 769 307 HOH HOH . H 4 HOH I 170 770 109 HOH HOH . H 4 HOH I 171 771 146 HOH HOH . H 4 HOH I 172 772 313 HOH HOH . H 4 HOH I 173 773 49 HOH HOH . H 4 HOH I 174 774 311 HOH HOH . H 4 HOH I 175 775 29 HOH HOH . H 4 HOH I 176 776 164 HOH HOH . H 4 HOH I 177 777 194 HOH HOH . H 4 HOH I 178 778 175 HOH HOH . H 4 HOH I 179 779 89 HOH HOH . H 4 HOH I 180 780 157 HOH HOH . H 4 HOH I 181 781 308 HOH HOH . H 4 HOH I 182 782 121 HOH HOH . H 4 HOH I 183 783 126 HOH HOH . H 4 HOH I 184 784 98 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 2 152.243 -77.95 2.366 1 47.43 ? N1 UDP 501 I 1 HETATM 2 C C2 UDP . . . B 2 152.717 -78.469 0.964 1 51.41 ? C2 UDP 501 I 1 HETATM 3 N N3 UDP . . . B 2 154.052 -79.18 0.999 1 49.73 ? N3 UDP 501 I 1 HETATM 4 C C4 UDP . . . B 2 154.804 -79.362 2.236 1 44.09 ? C4 UDP 501 I 1 HETATM 5 C C5 UDP . . . B 2 154.306 -78.869 3.458 1 47.87 ? C5 UDP 501 I 1 HETATM 6 C C6 UDP . . . B 2 153.04 -78.171 3.54 1 48.06 ? C6 UDP 501 I 1 HETATM 7 O O2 UDP . . . B 2 152.085 -78.313 -0.019 1 57.07 ? O2 UDP 501 I 1 HETATM 8 O O4 UDP . . . B 2 155.846 -79.928 2.216 1 47.55 ? O4 UDP 501 I 1 HETATM 9 C C1' UDP . . . B 2 151 -77.268 2.455 1 50.24 ? C1' UDP 501 I 1 HETATM 10 C C2' UDP . . . B 2 149.83 -78.338 2.997 1 55.21 ? C2' UDP 501 I 1 HETATM 11 O O2' UDP . . . B 2 149.108 -78.825 1.825 1 59.98 ? O2' UDP 501 I 1 HETATM 12 C C3' UDP . . . B 2 149.057 -77.715 3.782 1 51.83 ? C3' UDP 501 I 1 HETATM 13 C C4' UDP . . . B 2 149.748 -76.318 4.105 1 52.88 ? C4' UDP 501 I 1 HETATM 14 O O4' UDP . . . B 2 151.063 -76.287 3.29 1 50.33 ? O4' UDP 501 I 1 HETATM 15 O O3' UDP . . . B 2 147.738 -77.469 3.119 1 61.76 ? O3' UDP 501 I 1 HETATM 16 C C5' UDP . . . B 2 150.007 -76.186 5.461 1 46.3 ? C5' UDP 501 I 1 HETATM 17 O O5' UDP . . . B 2 150.714 -77.31 5.925 1 49.57 ? O5' UDP 501 I 1 HETATM 18 P PA UDP . . . B 2 150.809 -77.538 7.562 1 39.94 ? PA UDP 501 I 1 HETATM 19 O O1A UDP . . . B 2 151.981 -78.442 7.871 1 43.07 ? O1A UDP 501 I 1 HETATM 20 O O2A UDP . . . B 2 150.96 -76.185 8.225 1 40.4 ? O2A UDP 501 I 1 HETATM 21 O O3A UDP . . . B 2 149.397 -78.225 8.07 1 57.38 ? O3A UDP 501 I 1 HETATM 22 P PB UDP . . . B 2 148.754 -79.631 7.485 1 62.5 ? PB UDP 501 I 1 HETATM 23 O O1B UDP . . . B 2 147.707 -79.275 6.454 1 60.15 ? O1B UDP 501 I 1 HETATM 24 O O2B UDP . . . B 2 149.849 -80.458 6.856 1 57.86 ? O2B UDP 501 I 1 HETATM 25 O O3B UDP . . . B 2 148.128 -80.414 8.618 1 63.85 ? O3B UDP 501 I 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #