data_8WRJ # _model_server_result.job_id 8H_7srss60GcCOIK8fsoQA _model_server_result.datetime_utc '2024-11-29 03:23:46' _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 8wrj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 8WRJ # _exptl.entry_id 8WRJ _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 8WRJ _cell.length_a 46.022 _cell.length_b 53.005 _cell.length_c 200.795 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WRJ _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 ? _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 8WRJ _atom_sites.fract_transf_matrix[1][1] 0.021729 _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] 0.018866 _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] 0.00498 _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 6JI A 1 501 501 6JI DRG . C 3 UDP A 1 502 502 UDP UDP . D 4 HOH A 1 601 258 HOH HOH . D 4 HOH A 2 602 251 HOH HOH . D 4 HOH A 3 603 110 HOH HOH . D 4 HOH A 4 604 273 HOH HOH . D 4 HOH A 5 605 55 HOH HOH . D 4 HOH A 6 606 144 HOH HOH . D 4 HOH A 7 607 180 HOH HOH . D 4 HOH A 8 608 203 HOH HOH . D 4 HOH A 9 609 88 HOH HOH . D 4 HOH A 10 610 50 HOH HOH . D 4 HOH A 11 611 240 HOH HOH . D 4 HOH A 12 612 147 HOH HOH . D 4 HOH A 13 613 84 HOH HOH . D 4 HOH A 14 614 161 HOH HOH . D 4 HOH A 15 615 243 HOH HOH . D 4 HOH A 16 616 248 HOH HOH . D 4 HOH A 17 617 260 HOH HOH . D 4 HOH A 18 618 225 HOH HOH . D 4 HOH A 19 619 35 HOH HOH . D 4 HOH A 20 620 21 HOH HOH . D 4 HOH A 21 621 269 HOH HOH . D 4 HOH A 22 622 166 HOH HOH . D 4 HOH A 23 623 18 HOH HOH . D 4 HOH A 24 624 164 HOH HOH . D 4 HOH A 25 625 62 HOH HOH . D 4 HOH A 26 626 33 HOH HOH . D 4 HOH A 27 627 25 HOH HOH . D 4 HOH A 28 628 249 HOH HOH . D 4 HOH A 29 629 7 HOH HOH . D 4 HOH A 30 630 72 HOH HOH . D 4 HOH A 31 631 40 HOH HOH . D 4 HOH A 32 632 61 HOH HOH . D 4 HOH A 33 633 8 HOH HOH . D 4 HOH A 34 634 270 HOH HOH . D 4 HOH A 35 635 26 HOH HOH . D 4 HOH A 36 636 175 HOH HOH . D 4 HOH A 37 637 67 HOH HOH . D 4 HOH A 38 638 42 HOH HOH . D 4 HOH A 39 639 38 HOH HOH . D 4 HOH A 40 640 242 HOH HOH . D 4 HOH A 41 641 3 HOH HOH . D 4 HOH A 42 642 108 HOH HOH . D 4 HOH A 43 643 202 HOH HOH . D 4 HOH A 44 644 153 HOH HOH . D 4 HOH A 45 645 86 HOH HOH . D 4 HOH A 46 646 22 HOH HOH . D 4 HOH A 47 647 58 HOH HOH . D 4 HOH A 48 648 1 HOH HOH . D 4 HOH A 49 649 16 HOH HOH . D 4 HOH A 50 650 2 HOH HOH . D 4 HOH A 51 651 105 HOH HOH . D 4 HOH A 52 652 77 HOH HOH . D 4 HOH A 53 653 5 HOH HOH . D 4 HOH A 54 654 12 HOH HOH . D 4 HOH A 55 655 4 HOH HOH . D 4 HOH A 56 656 43 HOH HOH . D 4 HOH A 57 657 190 HOH HOH . D 4 HOH A 58 658 17 HOH HOH . D 4 HOH A 59 659 15 HOH HOH . D 4 HOH A 60 660 37 HOH HOH . D 4 HOH A 61 661 101 HOH HOH . D 4 HOH A 62 662 106 HOH HOH . D 4 HOH A 63 663 135 HOH HOH . D 4 HOH A 64 664 184 HOH HOH . D 4 HOH A 65 665 63 HOH HOH . D 4 HOH A 66 666 160 HOH HOH . D 4 HOH A 67 667 277 HOH HOH . D 4 HOH A 68 668 157 HOH HOH . D 4 HOH A 69 669 98 HOH HOH . D 4 HOH A 70 670 47 HOH HOH . D 4 HOH A 71 671 253 HOH HOH . D 4 HOH A 72 672 6 HOH HOH . D 4 HOH A 73 673 99 HOH HOH . D 4 HOH A 74 674 46 HOH HOH . D 4 HOH A 75 675 213 HOH HOH . D 4 HOH A 76 676 10 HOH HOH . D 4 HOH A 77 677 20 HOH HOH . D 4 HOH A 78 678 57 HOH HOH . D 4 HOH A 79 679 65 HOH HOH . D 4 HOH A 80 680 283 HOH HOH . D 4 HOH A 81 681 178 HOH HOH . D 4 HOH A 82 682 177 HOH HOH . D 4 HOH A 83 683 11 HOH HOH . D 4 HOH A 84 684 9 HOH HOH . D 4 HOH A 85 685 49 HOH HOH . D 4 HOH A 86 686 133 HOH HOH . D 4 HOH A 87 687 259 HOH HOH . D 4 HOH A 88 688 252 HOH HOH . D 4 HOH A 89 689 97 HOH HOH . D 4 HOH A 90 690 109 HOH HOH . D 4 HOH A 91 691 179 HOH HOH . D 4 HOH A 92 692 200 HOH HOH . D 4 HOH A 93 693 79 HOH HOH . D 4 HOH A 94 694 186 HOH HOH . D 4 HOH A 95 695 73 HOH HOH . D 4 HOH A 96 696 14 HOH HOH . D 4 HOH A 97 697 216 HOH HOH . D 4 HOH A 98 698 192 HOH HOH . D 4 HOH A 99 699 132 HOH HOH . D 4 HOH A 100 700 126 HOH HOH . D 4 HOH A 101 701 118 HOH HOH . D 4 HOH A 102 702 28 HOH HOH . D 4 HOH A 103 703 71 HOH HOH . D 4 HOH A 104 704 139 HOH HOH . D 4 HOH A 105 705 69 HOH HOH . D 4 HOH A 106 706 103 HOH HOH . D 4 HOH A 107 707 140 HOH HOH . D 4 HOH A 108 708 92 HOH HOH . D 4 HOH A 109 709 155 HOH HOH . D 4 HOH A 110 710 36 HOH HOH . D 4 HOH A 111 711 100 HOH HOH . D 4 HOH A 112 712 60 HOH HOH . D 4 HOH A 113 713 81 HOH HOH . D 4 HOH A 114 714 87 HOH HOH . D 4 HOH A 115 715 32 HOH HOH . D 4 HOH A 116 716 163 HOH HOH . D 4 HOH A 117 717 169 HOH HOH . D 4 HOH A 118 718 34 HOH HOH . D 4 HOH A 119 719 171 HOH HOH . D 4 HOH A 120 720 59 HOH HOH . D 4 HOH A 121 721 262 HOH HOH . D 4 HOH A 122 722 104 HOH HOH . D 4 HOH A 123 723 255 HOH HOH . D 4 HOH A 124 724 173 HOH HOH . D 4 HOH A 125 725 261 HOH HOH . D 4 HOH A 126 726 215 HOH HOH . D 4 HOH A 127 727 198 HOH HOH . D 4 HOH A 128 728 183 HOH HOH . D 4 HOH A 129 729 113 HOH HOH . D 4 HOH A 130 730 122 HOH HOH . D 4 HOH A 131 731 80 HOH HOH . D 4 HOH A 132 732 124 HOH HOH . D 4 HOH A 133 733 13 HOH HOH . D 4 HOH A 134 734 95 HOH HOH . D 4 HOH A 135 735 210 HOH HOH . D 4 HOH A 136 736 146 HOH HOH . D 4 HOH A 137 737 123 HOH HOH . D 4 HOH A 138 738 193 HOH HOH . D 4 HOH A 139 739 187 HOH HOH . D 4 HOH A 140 740 48 HOH HOH . D 4 HOH A 141 741 39 HOH HOH . D 4 HOH A 142 742 44 HOH HOH . D 4 HOH A 143 743 285 HOH HOH . D 4 HOH A 144 744 137 HOH HOH . D 4 HOH A 145 745 93 HOH HOH . D 4 HOH A 146 746 167 HOH HOH . D 4 HOH A 147 747 89 HOH HOH . D 4 HOH A 148 748 282 HOH HOH . D 4 HOH A 149 749 226 HOH HOH . D 4 HOH A 150 750 75 HOH HOH . D 4 HOH A 151 751 191 HOH HOH . D 4 HOH A 152 752 127 HOH HOH . D 4 HOH A 153 753 74 HOH HOH . D 4 HOH A 154 754 130 HOH HOH . D 4 HOH A 155 755 141 HOH HOH . D 4 HOH A 156 756 145 HOH HOH . D 4 HOH A 157 757 151 HOH HOH . D 4 HOH A 158 758 56 HOH HOH . D 4 HOH A 159 759 235 HOH HOH . D 4 HOH A 160 760 159 HOH HOH . D 4 HOH A 161 761 209 HOH HOH . D 4 HOH A 162 762 120 HOH HOH . D 4 HOH A 163 763 220 HOH HOH . D 4 HOH A 164 764 170 HOH HOH . D 4 HOH A 165 765 125 HOH HOH . D 4 HOH A 166 766 23 HOH HOH . D 4 HOH A 167 767 284 HOH HOH . D 4 HOH A 168 768 268 HOH HOH . D 4 HOH A 169 769 272 HOH HOH . D 4 HOH A 170 770 278 HOH HOH . D 4 HOH A 171 771 254 HOH HOH . D 4 HOH A 172 772 158 HOH HOH . D 4 HOH A 173 773 154 HOH HOH . D 4 HOH A 174 774 143 HOH HOH . D 4 HOH A 175 775 197 HOH HOH . D 4 HOH A 176 776 107 HOH HOH . D 4 HOH A 177 777 222 HOH HOH . D 4 HOH A 178 778 239 HOH HOH . D 4 HOH A 179 779 241 HOH HOH . D 4 HOH A 180 780 246 HOH HOH . D 4 HOH A 181 781 199 HOH HOH . D 4 HOH A 182 782 70 HOH HOH . D 4 HOH A 183 783 83 HOH HOH . D 4 HOH A 184 784 205 HOH HOH . D 4 HOH A 185 785 31 HOH HOH . D 4 HOH A 186 786 276 HOH HOH . D 4 HOH A 187 787 230 HOH HOH . D 4 HOH A 188 788 218 HOH HOH . D 4 HOH A 189 789 182 HOH HOH . D 4 HOH A 190 790 206 HOH HOH . D 4 HOH A 191 791 217 HOH HOH . D 4 HOH A 192 792 85 HOH HOH . D 4 HOH A 193 793 264 HOH HOH . D 4 HOH A 194 794 219 HOH HOH . D 4 HOH A 195 795 168 HOH HOH . D 4 HOH A 196 796 227 HOH HOH . D 4 HOH A 197 797 142 HOH HOH . D 4 HOH A 198 798 245 HOH HOH . D 4 HOH A 199 799 281 HOH HOH . D 4 HOH A 200 800 82 HOH HOH . D 4 HOH A 201 801 201 HOH HOH . D 4 HOH A 202 802 149 HOH HOH . D 4 HOH A 203 803 232 HOH HOH . D 4 HOH A 204 804 238 HOH HOH . D 4 HOH A 205 805 257 HOH HOH . D 4 HOH A 206 806 280 HOH HOH . D 4 HOH A 207 807 115 HOH HOH . D 4 HOH A 208 808 138 HOH HOH . D 4 HOH A 209 809 189 HOH HOH . D 4 HOH A 210 810 94 HOH HOH . D 4 HOH A 211 811 275 HOH HOH . D 4 HOH A 212 812 271 HOH HOH . D 4 HOH A 213 813 224 HOH HOH . D 4 HOH A 214 814 24 HOH HOH . D 4 HOH A 215 815 279 HOH HOH . D 4 HOH A 216 816 76 HOH HOH . D 4 HOH A 217 817 266 HOH HOH . D 4 HOH A 218 818 223 HOH HOH . D 4 HOH A 219 819 185 HOH HOH . D 4 HOH A 220 820 131 HOH HOH . D 4 HOH A 221 821 181 HOH HOH . D 4 HOH A 222 822 207 HOH HOH . D 4 HOH A 223 823 234 HOH HOH . D 4 HOH A 224 824 247 HOH HOH . D 4 HOH A 225 825 263 HOH HOH . D 4 HOH A 226 826 196 HOH HOH . D 4 HOH A 227 827 174 HOH HOH . D 4 HOH A 228 828 267 HOH HOH . D 4 HOH A 229 829 229 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 -4.162 21.259 80.572 1 19.67 ? N1 UDP 502 A 1 HETATM 2 C C2 UDP . . . C 3 -3.071 20.726 81.081 1 21.33 ? C2 UDP 502 A 1 HETATM 3 N N3 UDP . . . C 3 -2.385 21.316 82.053 1 21.81 ? N3 UDP 502 A 1 HETATM 4 C C4 UDP . . . C 3 -2.815 22.477 82.522 1 20.4 ? C4 UDP 502 A 1 HETATM 5 C C5 UDP . . . C 3 -3.965 23.079 82.014 1 20.7 ? C5 UDP 502 A 1 HETATM 6 C C6 UDP . . . C 3 -4.637 22.421 80.991 1 19.41 ? C6 UDP 502 A 1 HETATM 7 O O2 UDP . . . C 3 -2.612 19.498 80.594 1 19.91 ? O2 UDP 502 A 1 HETATM 8 O O4 UDP . . . C 3 -2.11 23.103 83.531 1 21.57 ? O4 UDP 502 A 1 HETATM 9 C C1' UDP . . . C 3 -4.854 20.587 79.452 1 21.31 ? C1' UDP 502 A 1 HETATM 10 C C2' UDP . . . C 3 -6.257 20.086 79.795 1 19.15 ? C2' UDP 502 A 1 HETATM 11 O O2' UDP . . . C 3 -6.165 18.786 80.225 1 21.44 ? O2' UDP 502 A 1 HETATM 12 C C3' UDP . . . C 3 -6.96 20.211 78.421 1 19.24 ? C3' UDP 502 A 1 HETATM 13 C C4' UDP . . . C 3 -6.434 21.261 77.816 1 19.37 ? C4' UDP 502 A 1 HETATM 14 O O4' UDP . . . C 3 -5.011 21.506 78.508 1 20.76 ? O4' UDP 502 A 1 HETATM 15 O O3' UDP . . . C 3 -6.546 19.033 77.622 1 23.12 ? O3' UDP 502 A 1 HETATM 16 C C5' UDP . . . C 3 -7.285 22.512 77.936 1 19.81 ? C5' UDP 502 A 1 HETATM 17 O O5' UDP . . . C 3 -8.381 22.289 77.094 1 19.44 ? O5' UDP 502 A 1 HETATM 18 P PA UDP . . . C 3 -9.819 23.034 77.352 1 20.1 ? PA UDP 502 A 1 HETATM 19 O O1A UDP . . . C 3 -10.871 22.569 76.367 1 19.66 ? O1A UDP 502 A 1 HETATM 20 O O2A UDP . . . C 3 -10.241 22.85 78.788 1 19.85 -1 O2A UDP 502 A 1 HETATM 21 O O3A UDP . . . C 3 -9.639 24.647 77.223 1 20.69 ? O3A UDP 502 A 1 HETATM 22 P PB UDP . . . C 3 -8.841 25.517 76.115 1 21.96 ? PB UDP 502 A 1 HETATM 23 O O1B UDP . . . C 3 -9.071 24.953 74.724 1 18.96 ? O1B UDP 502 A 1 HETATM 24 O O2B UDP . . . C 3 -7.388 25.61 76.473 1 22.43 -1 O2B UDP 502 A 1 HETATM 25 O O3B UDP . . . C 3 -9.504 26.878 76.158 1 21.33 ? O3B UDP 502 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #