data_9KSW # _model_server_result.job_id wk6blx_QBe-l5GWwiStkpw _model_server_result.datetime_utc '2025-07-08 00:09:36' _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 9ksw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 9KSW # _exptl.entry_id 9KSW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 9KSW _cell.length_a 80.342 _cell.length_b 120.505 _cell.length_c 47.794 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9KSW _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 _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 # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _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 U5P sing 435 n n N1 C6 U5P sing 436 n n N1 C1' U5P sing 437 n n C2 N3 U5P sing 438 n n C2 O2 U5P doub 439 n n N3 C4 U5P sing 440 n n N3 HN3 U5P sing 441 n n C4 C5 U5P sing 442 n n C4 O4 U5P doub 443 n n C5 C6 U5P doub 444 n n C5 H5 U5P sing 445 n n C6 H6 U5P sing 446 n n C1' C2' U5P sing 447 n n C1' O4' U5P sing 448 n n C1' H1' U5P sing 449 n n C2' O2' U5P sing 450 n n C2' C3' U5P sing 451 n n C2' H2' U5P sing 452 n n O2' HO2' U5P sing 453 n n C3' C4' U5P sing 454 n n C3' O3' U5P sing 455 n n C3' H3' U5P sing 456 n n C4' O4' U5P sing 457 n n C4' C5' U5P sing 458 n n C4' H4' U5P sing 459 n n O3' HO3' U5P sing 460 n n C5' O5' U5P sing 461 n n C5' "H5'1" U5P sing 462 n n C5' "H5'2" U5P sing 463 n n O5' P U5P sing 464 n n P O1P U5P doub 465 n n P O2P U5P sing 466 n n P O3P U5P sing 467 n n O2P HOP2 U5P sing 468 n n O3P HOP3 U5P sing 469 n n # _atom_sites.entry_id 9KSW _atom_sites.fract_transf_matrix[1][1] 0.012447 _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] 0.008298 _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] 0.020923 _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 U5P A 1 501 504 U5P UMP . C 3 RUT A 1 502 505 RUT RUT . D 4 HOH A 1 601 26 HOH HOH . D 4 HOH A 2 602 33 HOH HOH . D 4 HOH A 3 603 83 HOH HOH . D 4 HOH A 4 604 239 HOH HOH . D 4 HOH A 5 605 228 HOH HOH . D 4 HOH A 6 606 34 HOH HOH . D 4 HOH A 7 607 6 HOH HOH . D 4 HOH A 8 608 56 HOH HOH . D 4 HOH A 9 609 135 HOH HOH . D 4 HOH A 10 610 105 HOH HOH . D 4 HOH A 11 611 65 HOH HOH . D 4 HOH A 12 612 186 HOH HOH . D 4 HOH A 13 613 132 HOH HOH . D 4 HOH A 14 614 49 HOH HOH . D 4 HOH A 15 615 100 HOH HOH . D 4 HOH A 16 616 188 HOH HOH . D 4 HOH A 17 617 75 HOH HOH . D 4 HOH A 18 618 111 HOH HOH . D 4 HOH A 19 619 175 HOH HOH . D 4 HOH A 20 620 231 HOH HOH . D 4 HOH A 21 621 90 HOH HOH . D 4 HOH A 22 622 224 HOH HOH . D 4 HOH A 23 623 106 HOH HOH . D 4 HOH A 24 624 16 HOH HOH . D 4 HOH A 25 625 196 HOH HOH . D 4 HOH A 26 626 119 HOH HOH . D 4 HOH A 27 627 81 HOH HOH . D 4 HOH A 28 628 84 HOH HOH . D 4 HOH A 29 629 36 HOH HOH . D 4 HOH A 30 630 150 HOH HOH . D 4 HOH A 31 631 94 HOH HOH . D 4 HOH A 32 632 46 HOH HOH . D 4 HOH A 33 633 128 HOH HOH . D 4 HOH A 34 634 131 HOH HOH . D 4 HOH A 35 635 88 HOH HOH . D 4 HOH A 36 636 113 HOH HOH . D 4 HOH A 37 637 169 HOH HOH . D 4 HOH A 38 638 7 HOH HOH . D 4 HOH A 39 639 197 HOH HOH . D 4 HOH A 40 640 86 HOH HOH . D 4 HOH A 41 641 160 HOH HOH . D 4 HOH A 42 642 50 HOH HOH . D 4 HOH A 43 643 2 HOH HOH . D 4 HOH A 44 644 15 HOH HOH . D 4 HOH A 45 645 32 HOH HOH . D 4 HOH A 46 646 54 HOH HOH . D 4 HOH A 47 647 31 HOH HOH . D 4 HOH A 48 648 104 HOH HOH . D 4 HOH A 49 649 25 HOH HOH . D 4 HOH A 50 650 4 HOH HOH . D 4 HOH A 51 651 210 HOH HOH . D 4 HOH A 52 652 237 HOH HOH . D 4 HOH A 53 653 13 HOH HOH . D 4 HOH A 54 654 120 HOH HOH . D 4 HOH A 55 655 110 HOH HOH . D 4 HOH A 56 656 126 HOH HOH . D 4 HOH A 57 657 199 HOH HOH . D 4 HOH A 58 658 67 HOH HOH . D 4 HOH A 59 659 35 HOH HOH . D 4 HOH A 60 660 41 HOH HOH . D 4 HOH A 61 661 45 HOH HOH . D 4 HOH A 62 662 125 HOH HOH . D 4 HOH A 63 663 43 HOH HOH . D 4 HOH A 64 664 28 HOH HOH . D 4 HOH A 65 665 79 HOH HOH . D 4 HOH A 66 666 139 HOH HOH . D 4 HOH A 67 667 153 HOH HOH . D 4 HOH A 68 668 138 HOH HOH . D 4 HOH A 69 669 198 HOH HOH . D 4 HOH A 70 670 240 HOH HOH . D 4 HOH A 71 671 66 HOH HOH . D 4 HOH A 72 672 70 HOH HOH . D 4 HOH A 73 673 60 HOH HOH . D 4 HOH A 74 674 78 HOH HOH . D 4 HOH A 75 675 96 HOH HOH . D 4 HOH A 76 676 80 HOH HOH . D 4 HOH A 77 677 194 HOH HOH . D 4 HOH A 78 678 68 HOH HOH . D 4 HOH A 79 679 115 HOH HOH . D 4 HOH A 80 680 92 HOH HOH . D 4 HOH A 81 681 129 HOH HOH . D 4 HOH A 82 682 21 HOH HOH . D 4 HOH A 83 683 144 HOH HOH . D 4 HOH A 84 684 215 HOH HOH . D 4 HOH A 85 685 10 HOH HOH . D 4 HOH A 86 686 38 HOH HOH . D 4 HOH A 87 687 12 HOH HOH . D 4 HOH A 88 688 134 HOH HOH . D 4 HOH A 89 689 40 HOH HOH . D 4 HOH A 90 690 19 HOH HOH . D 4 HOH A 91 691 191 HOH HOH . D 4 HOH A 92 692 95 HOH HOH . D 4 HOH A 93 693 234 HOH HOH . D 4 HOH A 94 694 151 HOH HOH . D 4 HOH A 95 695 1 HOH HOH . D 4 HOH A 96 696 123 HOH HOH . D 4 HOH A 97 697 3 HOH HOH . D 4 HOH A 98 698 112 HOH HOH . D 4 HOH A 99 699 14 HOH HOH . D 4 HOH A 100 700 168 HOH HOH . D 4 HOH A 101 701 17 HOH HOH . D 4 HOH A 102 702 39 HOH HOH . D 4 HOH A 103 703 62 HOH HOH . D 4 HOH A 104 704 29 HOH HOH . D 4 HOH A 105 705 37 HOH HOH . D 4 HOH A 106 706 5 HOH HOH . D 4 HOH A 107 707 241 HOH HOH . D 4 HOH A 108 708 117 HOH HOH . D 4 HOH A 109 709 47 HOH HOH . D 4 HOH A 110 710 143 HOH HOH . D 4 HOH A 111 711 163 HOH HOH . D 4 HOH A 112 712 233 HOH HOH . D 4 HOH A 113 713 61 HOH HOH . D 4 HOH A 114 714 147 HOH HOH . D 4 HOH A 115 715 18 HOH HOH . D 4 HOH A 116 716 137 HOH HOH . D 4 HOH A 117 717 181 HOH HOH . D 4 HOH A 118 718 57 HOH HOH . D 4 HOH A 119 719 63 HOH HOH . D 4 HOH A 120 720 185 HOH HOH . D 4 HOH A 121 721 118 HOH HOH . D 4 HOH A 122 722 42 HOH HOH . D 4 HOH A 123 723 76 HOH HOH . D 4 HOH A 124 724 192 HOH HOH . D 4 HOH A 125 725 8 HOH HOH . D 4 HOH A 126 726 72 HOH HOH . D 4 HOH A 127 727 232 HOH HOH . D 4 HOH A 128 728 189 HOH HOH . D 4 HOH A 129 729 204 HOH HOH . D 4 HOH A 130 730 220 HOH HOH . D 4 HOH A 131 731 184 HOH HOH . D 4 HOH A 132 732 53 HOH HOH . D 4 HOH A 133 733 170 HOH HOH . D 4 HOH A 134 734 167 HOH HOH . D 4 HOH A 135 735 207 HOH HOH . D 4 HOH A 136 736 9 HOH HOH . D 4 HOH A 137 737 158 HOH HOH . D 4 HOH A 138 738 101 HOH HOH . D 4 HOH A 139 739 22 HOH HOH . D 4 HOH A 140 740 107 HOH HOH . D 4 HOH A 141 741 64 HOH HOH . D 4 HOH A 142 742 20 HOH HOH . D 4 HOH A 143 743 203 HOH HOH . D 4 HOH A 144 744 74 HOH HOH . D 4 HOH A 145 745 122 HOH HOH . D 4 HOH A 146 746 30 HOH HOH . D 4 HOH A 147 747 200 HOH HOH . D 4 HOH A 148 748 219 HOH HOH . D 4 HOH A 149 749 73 HOH HOH . D 4 HOH A 150 750 24 HOH HOH . D 4 HOH A 151 751 161 HOH HOH . D 4 HOH A 152 752 130 HOH HOH . D 4 HOH A 153 753 58 HOH HOH . D 4 HOH A 154 754 236 HOH HOH . D 4 HOH A 155 755 190 HOH HOH . D 4 HOH A 156 756 27 HOH HOH . D 4 HOH A 157 757 230 HOH HOH . D 4 HOH A 158 758 141 HOH HOH . D 4 HOH A 159 759 48 HOH HOH . D 4 HOH A 160 760 59 HOH HOH . D 4 HOH A 161 761 82 HOH HOH . D 4 HOH A 162 762 99 HOH HOH . D 4 HOH A 163 763 69 HOH HOH . D 4 HOH A 164 764 225 HOH HOH . D 4 HOH A 165 765 114 HOH HOH . D 4 HOH A 166 766 87 HOH HOH . D 4 HOH A 167 767 213 HOH HOH . D 4 HOH A 168 768 202 HOH HOH . D 4 HOH A 169 769 98 HOH HOH . D 4 HOH A 170 770 11 HOH HOH . D 4 HOH A 171 771 89 HOH HOH . D 4 HOH A 172 772 140 HOH HOH . D 4 HOH A 173 773 149 HOH HOH . D 4 HOH A 174 774 124 HOH HOH . D 4 HOH A 175 775 116 HOH HOH . D 4 HOH A 176 776 51 HOH HOH . D 4 HOH A 177 777 180 HOH HOH . D 4 HOH A 178 778 55 HOH HOH . D 4 HOH A 179 779 166 HOH HOH . D 4 HOH A 180 780 177 HOH HOH . D 4 HOH A 181 781 146 HOH HOH . D 4 HOH A 182 782 23 HOH HOH . D 4 HOH A 183 783 97 HOH HOH . D 4 HOH A 184 784 178 HOH HOH . D 4 HOH A 185 785 187 HOH HOH . D 4 HOH A 186 786 218 HOH HOH . D 4 HOH A 187 787 155 HOH HOH . D 4 HOH A 188 788 136 HOH HOH . D 4 HOH A 189 789 44 HOH HOH . D 4 HOH A 190 790 156 HOH HOH . D 4 HOH A 191 791 52 HOH HOH . D 4 HOH A 192 792 145 HOH HOH . D 4 HOH A 193 793 71 HOH HOH . D 4 HOH A 194 794 109 HOH HOH . D 4 HOH A 195 795 195 HOH HOH . D 4 HOH A 196 796 93 HOH HOH . D 4 HOH A 197 797 133 HOH HOH . D 4 HOH A 198 798 223 HOH HOH . D 4 HOH A 199 799 211 HOH HOH . D 4 HOH A 200 800 214 HOH HOH . D 4 HOH A 201 801 242 HOH HOH . D 4 HOH A 202 802 206 HOH HOH . D 4 HOH A 203 803 212 HOH HOH . D 4 HOH A 204 804 193 HOH HOH . D 4 HOH A 205 805 121 HOH HOH . D 4 HOH A 206 806 226 HOH HOH . D 4 HOH A 207 807 108 HOH HOH . D 4 HOH A 208 808 208 HOH HOH . D 4 HOH A 209 809 209 HOH HOH . D 4 HOH A 210 810 182 HOH HOH . D 4 HOH A 211 811 127 HOH HOH . D 4 HOH A 212 812 205 HOH HOH . D 4 HOH A 213 813 103 HOH HOH . D 4 HOH A 214 814 159 HOH HOH . D 4 HOH A 215 815 183 HOH HOH . D 4 HOH A 216 816 235 HOH HOH . D 4 HOH A 217 817 172 HOH HOH . D 4 HOH A 218 818 179 HOH HOH . D 4 HOH A 219 819 171 HOH HOH . D 4 HOH A 220 820 173 HOH HOH . D 4 HOH A 221 821 229 HOH HOH . D 4 HOH A 222 822 102 HOH HOH . D 4 HOH A 223 823 85 HOH HOH . D 4 HOH A 224 824 217 HOH HOH . D 4 HOH A 225 825 165 HOH HOH . D 4 HOH A 226 826 77 HOH HOH . D 4 HOH A 227 827 222 HOH HOH . D 4 HOH A 228 828 201 HOH HOH . D 4 HOH A 229 829 221 HOH HOH . D 4 HOH A 230 830 152 HOH HOH . D 4 HOH A 231 831 142 HOH HOH . D 4 HOH A 232 832 157 HOH HOH . D 4 HOH A 233 833 154 HOH HOH . D 4 HOH A 234 834 238 HOH HOH . D 4 HOH A 235 835 174 HOH HOH . D 4 HOH A 236 836 227 HOH HOH . D 4 HOH A 237 837 148 HOH HOH . D 4 HOH A 238 838 176 HOH HOH . D 4 HOH A 239 839 91 HOH HOH . D 4 HOH A 240 840 216 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 U5P . . . B 2 -16.774 30.42 15.173 1 27.52 ? N1 U5P 501 A 1 HETATM 2 C C2 U5P . . . B 2 -17.826 31.223 15.58 1 24.2 ? C2 U5P 501 A 1 HETATM 3 N N3 U5P . . . B 2 -17.461 32.34 16.283 1 20.4 ? N3 U5P 501 A 1 HETATM 4 C C4 U5P . . . B 2 -16.183 32.702 16.663 1 25.23 ? C4 U5P 501 A 1 HETATM 5 C C5 U5P . . . B 2 -15.146 31.807 16.231 1 23.44 ? C5 U5P 501 A 1 HETATM 6 C C6 U5P . . . B 2 -15.472 30.716 15.517 1 23.89 ? C6 U5P 501 A 1 HETATM 7 O O2 U5P . . . B 2 -18.992 30.985 15.298 1 23.63 ? O2 U5P 501 A 1 HETATM 8 O O4 U5P . . . B 2 -16.027 33.739 17.306 1 24.34 ? O4 U5P 501 A 1 HETATM 9 C C1' U5P . . . B 2 -17.119 29.188 14.432 1 26.36 ? C1' U5P 501 A 1 HETATM 10 C C2' U5P . . . B 2 -16.832 29.226 12.93 1 28.32 ? C2' U5P 501 A 1 HETATM 11 O O2' U5P . . . B 2 -17.911 29.799 12.221 1 21.79 ? O2' U5P 501 A 1 HETATM 12 C C3' U5P . . . B 2 -16.683 27.727 12.633 1 29.03 ? C3' U5P 501 A 1 HETATM 13 C C4' U5P . . . B 2 -15.973 27.216 13.898 1 25.47 ? C4' U5P 501 A 1 HETATM 14 O O3' U5P . . . B 2 -17.952 27.104 12.476 1 28.11 ? O3' U5P 501 A 1 HETATM 15 O O4' U5P . . . B 2 -16.344 28.134 14.956 1 26.96 ? O4' U5P 501 A 1 HETATM 16 C C5' U5P . . . B 2 -14.471 27.179 13.808 1 31.7 ? C5' U5P 501 A 1 HETATM 17 O O5' U5P . . . B 2 -14.141 26.084 12.943 1 27.02 ? O5' U5P 501 A 1 HETATM 18 P P U5P . . . B 2 -12.79 26.133 12.091 1 25.48 ? P U5P 501 A 1 HETATM 19 O O1P U5P . . . B 2 -11.633 26.329 13.067 1 29.08 -1 O1P U5P 501 A 1 HETATM 20 O O2P U5P . . . B 2 -12.925 27.282 11.122 1 20.51 ? O2P U5P 501 A 1 HETATM 21 O O3P U5P . . . B 2 -12.792 24.759 11.415 1 16.81 -1 O3P U5P 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #