data_8INA # _model_server_result.job_id Q8StODH4A_eiWS1ilBk9YA _model_server_result.datetime_utc '2024-12-01 12:18:49' _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 8ina # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8INA # _exptl.entry_id 8INA _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 8INA _cell.length_a 45.741 _cell.length_b 52.667 _cell.length_c 202.111 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8INA _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 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 371 n n N1 C6 UDP sing 372 n n N1 C1' UDP sing 373 n n C2 N3 UDP sing 374 n n C2 O2 UDP doub 375 n n N3 C4 UDP sing 376 n n N3 HN3 UDP sing 377 n n C4 C5 UDP sing 378 n n C4 O4 UDP doub 379 n n C5 C6 UDP doub 380 n n C5 H5 UDP sing 381 n n C6 H6 UDP sing 382 n n C1' C2' UDP sing 383 n n C1' O4' UDP sing 384 n n C1' H1' UDP sing 385 n n C2' O2' UDP sing 386 n n C2' C3' UDP sing 387 n n C2' H2' UDP sing 388 n n O2' HO2' UDP sing 389 n n C3' C4' UDP sing 390 n n C3' O3' UDP sing 391 n n C3' H3' UDP sing 392 n n C4' O4' UDP sing 393 n n C4' C5' UDP sing 394 n n C4' H4' UDP sing 395 n n O3' HO3' UDP sing 396 n n C5' O5' UDP sing 397 n n C5' "H5'1" UDP sing 398 n n C5' "H5'2" UDP sing 399 n n O5' PA UDP sing 400 n n PA O1A UDP doub 401 n n PA O2A UDP sing 402 n n PA O3A UDP sing 403 n n O2A HOA2 UDP sing 404 n n O3A PB UDP sing 405 n n PB O1B UDP doub 406 n n PB O2B UDP sing 407 n n PB O3B UDP sing 408 n n O2B HOB2 UDP sing 409 n n O3B HOB3 UDP sing 410 n n # _atom_sites.entry_id 8INA _atom_sites.fract_transf_matrix[1][1] 0.021862 _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] 0.018987 _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] 0.004948 _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 1 501 501 UDP UDP . C 3 GOL A 1 502 502 GOL GRG . D 4 HOH A 1 601 86 HOH HOH . D 4 HOH A 2 602 117 HOH HOH . D 4 HOH A 3 603 168 HOH HOH . D 4 HOH A 4 604 81 HOH HOH . D 4 HOH A 5 605 85 HOH HOH . D 4 HOH A 6 606 274 HOH HOH . D 4 HOH A 7 607 131 HOH HOH . D 4 HOH A 8 608 175 HOH HOH . D 4 HOH A 9 609 24 HOH HOH . D 4 HOH A 10 610 89 HOH HOH . D 4 HOH A 11 611 269 HOH HOH . D 4 HOH A 12 612 132 HOH HOH . D 4 HOH A 13 613 130 HOH HOH . D 4 HOH A 14 614 18 HOH HOH . D 4 HOH A 15 615 52 HOH HOH . D 4 HOH A 16 616 116 HOH HOH . D 4 HOH A 17 617 61 HOH HOH . D 4 HOH A 18 618 77 HOH HOH . D 4 HOH A 19 619 133 HOH HOH . D 4 HOH A 20 620 207 HOH HOH . D 4 HOH A 21 621 252 HOH HOH . D 4 HOH A 22 622 152 HOH HOH . D 4 HOH A 23 623 236 HOH HOH . D 4 HOH A 24 624 68 HOH HOH . D 4 HOH A 25 625 33 HOH HOH . D 4 HOH A 26 626 143 HOH HOH . D 4 HOH A 27 627 129 HOH HOH . D 4 HOH A 28 628 10 HOH HOH . D 4 HOH A 29 629 70 HOH HOH . D 4 HOH A 30 630 215 HOH HOH . D 4 HOH A 31 631 226 HOH HOH . D 4 HOH A 32 632 65 HOH HOH . D 4 HOH A 33 633 166 HOH HOH . D 4 HOH A 34 634 275 HOH HOH . D 4 HOH A 35 635 87 HOH HOH . D 4 HOH A 36 636 113 HOH HOH . D 4 HOH A 37 637 124 HOH HOH . D 4 HOH A 38 638 109 HOH HOH . D 4 HOH A 39 639 3 HOH HOH . D 4 HOH A 40 640 66 HOH HOH . D 4 HOH A 41 641 2 HOH HOH . D 4 HOH A 42 642 200 HOH HOH . D 4 HOH A 43 643 7 HOH HOH . D 4 HOH A 44 644 121 HOH HOH . D 4 HOH A 45 645 95 HOH HOH . D 4 HOH A 46 646 229 HOH HOH . D 4 HOH A 47 647 16 HOH HOH . D 4 HOH A 48 648 149 HOH HOH . D 4 HOH A 49 649 39 HOH HOH . D 4 HOH A 50 650 158 HOH HOH . D 4 HOH A 51 651 26 HOH HOH . D 4 HOH A 52 652 102 HOH HOH . D 4 HOH A 53 653 108 HOH HOH . D 4 HOH A 54 654 8 HOH HOH . D 4 HOH A 55 655 153 HOH HOH . D 4 HOH A 56 656 1 HOH HOH . D 4 HOH A 57 657 181 HOH HOH . D 4 HOH A 58 658 249 HOH HOH . D 4 HOH A 59 659 257 HOH HOH . D 4 HOH A 60 660 63 HOH HOH . D 4 HOH A 61 661 43 HOH HOH . D 4 HOH A 62 662 94 HOH HOH . D 4 HOH A 63 663 221 HOH HOH . D 4 HOH A 64 664 28 HOH HOH . D 4 HOH A 65 665 140 HOH HOH . D 4 HOH A 66 666 37 HOH HOH . D 4 HOH A 67 667 34 HOH HOH . D 4 HOH A 68 668 36 HOH HOH . D 4 HOH A 69 669 104 HOH HOH . D 4 HOH A 70 670 101 HOH HOH . D 4 HOH A 71 671 75 HOH HOH . D 4 HOH A 72 672 22 HOH HOH . D 4 HOH A 73 673 35 HOH HOH . D 4 HOH A 74 674 165 HOH HOH . D 4 HOH A 75 675 5 HOH HOH . D 4 HOH A 76 676 32 HOH HOH . D 4 HOH A 77 677 255 HOH HOH . D 4 HOH A 78 678 25 HOH HOH . D 4 HOH A 79 679 38 HOH HOH . D 4 HOH A 80 680 21 HOH HOH . D 4 HOH A 81 681 44 HOH HOH . D 4 HOH A 82 682 73 HOH HOH . D 4 HOH A 83 683 179 HOH HOH . D 4 HOH A 84 684 58 HOH HOH . D 4 HOH A 85 685 218 HOH HOH . D 4 HOH A 86 686 189 HOH HOH . D 4 HOH A 87 687 134 HOH HOH . D 4 HOH A 88 688 92 HOH HOH . D 4 HOH A 89 689 72 HOH HOH . D 4 HOH A 90 690 20 HOH HOH . D 4 HOH A 91 691 12 HOH HOH . D 4 HOH A 92 692 55 HOH HOH . D 4 HOH A 93 693 114 HOH HOH . D 4 HOH A 94 694 6 HOH HOH . D 4 HOH A 95 695 107 HOH HOH . D 4 HOH A 96 696 99 HOH HOH . D 4 HOH A 97 697 67 HOH HOH . D 4 HOH A 98 698 151 HOH HOH . D 4 HOH A 99 699 120 HOH HOH . D 4 HOH A 100 700 258 HOH HOH . D 4 HOH A 101 701 186 HOH HOH . D 4 HOH A 102 702 119 HOH HOH . D 4 HOH A 103 703 11 HOH HOH . D 4 HOH A 104 704 176 HOH HOH . D 4 HOH A 105 705 23 HOH HOH . D 4 HOH A 106 706 259 HOH HOH . D 4 HOH A 107 707 272 HOH HOH . D 4 HOH A 108 708 54 HOH HOH . D 4 HOH A 109 709 174 HOH HOH . D 4 HOH A 110 710 45 HOH HOH . D 4 HOH A 111 711 17 HOH HOH . D 4 HOH A 112 712 62 HOH HOH . D 4 HOH A 113 713 123 HOH HOH . D 4 HOH A 114 714 48 HOH HOH . D 4 HOH A 115 715 88 HOH HOH . D 4 HOH A 116 716 90 HOH HOH . D 4 HOH A 117 717 205 HOH HOH . D 4 HOH A 118 718 159 HOH HOH . D 4 HOH A 119 719 106 HOH HOH . D 4 HOH A 120 720 47 HOH HOH . D 4 HOH A 121 721 212 HOH HOH . D 4 HOH A 122 722 183 HOH HOH . D 4 HOH A 123 723 9 HOH HOH . D 4 HOH A 124 724 15 HOH HOH . D 4 HOH A 125 725 71 HOH HOH . D 4 HOH A 126 726 198 HOH HOH . D 4 HOH A 127 727 4 HOH HOH . D 4 HOH A 128 728 201 HOH HOH . D 4 HOH A 129 729 214 HOH HOH . D 4 HOH A 130 730 266 HOH HOH . D 4 HOH A 131 731 156 HOH HOH . D 4 HOH A 132 732 19 HOH HOH . D 4 HOH A 133 733 180 HOH HOH . D 4 HOH A 134 734 139 HOH HOH . D 4 HOH A 135 735 57 HOH HOH . D 4 HOH A 136 736 59 HOH HOH . D 4 HOH A 137 737 250 HOH HOH . D 4 HOH A 138 738 53 HOH HOH . D 4 HOH A 139 739 172 HOH HOH . D 4 HOH A 140 740 127 HOH HOH . D 4 HOH A 141 741 248 HOH HOH . D 4 HOH A 142 742 208 HOH HOH . D 4 HOH A 143 743 163 HOH HOH . D 4 HOH A 144 744 97 HOH HOH . D 4 HOH A 145 745 190 HOH HOH . D 4 HOH A 146 746 233 HOH HOH . D 4 HOH A 147 747 164 HOH HOH . D 4 HOH A 148 748 69 HOH HOH . D 4 HOH A 149 749 42 HOH HOH . D 4 HOH A 150 750 60 HOH HOH . D 4 HOH A 151 751 14 HOH HOH . D 4 HOH A 152 752 251 HOH HOH . D 4 HOH A 153 753 144 HOH HOH . D 4 HOH A 154 754 105 HOH HOH . D 4 HOH A 155 755 238 HOH HOH . D 4 HOH A 156 756 74 HOH HOH . D 4 HOH A 157 757 194 HOH HOH . D 4 HOH A 158 758 147 HOH HOH . D 4 HOH A 159 759 78 HOH HOH . D 4 HOH A 160 760 46 HOH HOH . D 4 HOH A 161 761 126 HOH HOH . D 4 HOH A 162 762 40 HOH HOH . D 4 HOH A 163 763 136 HOH HOH . D 4 HOH A 164 764 177 HOH HOH . D 4 HOH A 165 765 111 HOH HOH . D 4 HOH A 166 766 241 HOH HOH . D 4 HOH A 167 767 83 HOH HOH . D 4 HOH A 168 768 264 HOH HOH . D 4 HOH A 169 769 173 HOH HOH . D 4 HOH A 170 770 199 HOH HOH . D 4 HOH A 171 771 49 HOH HOH . D 4 HOH A 172 772 27 HOH HOH . D 4 HOH A 173 773 217 HOH HOH . D 4 HOH A 174 774 203 HOH HOH . D 4 HOH A 175 775 31 HOH HOH . D 4 HOH A 176 776 80 HOH HOH . D 4 HOH A 177 777 13 HOH HOH . D 4 HOH A 178 778 178 HOH HOH . D 4 HOH A 179 779 242 HOH HOH . D 4 HOH A 180 780 267 HOH HOH . D 4 HOH A 181 781 167 HOH HOH . D 4 HOH A 182 782 243 HOH HOH . D 4 HOH A 183 783 146 HOH HOH . D 4 HOH A 184 784 265 HOH HOH . D 4 HOH A 185 785 230 HOH HOH . D 4 HOH A 186 786 184 HOH HOH . D 4 HOH A 187 787 56 HOH HOH . D 4 HOH A 188 788 98 HOH HOH . D 4 HOH A 189 789 162 HOH HOH . D 4 HOH A 190 790 103 HOH HOH . D 4 HOH A 191 791 76 HOH HOH . D 4 HOH A 192 792 246 HOH HOH . D 4 HOH A 193 793 160 HOH HOH . D 4 HOH A 194 794 188 HOH HOH . D 4 HOH A 195 795 195 HOH HOH . D 4 HOH A 196 796 187 HOH HOH . D 4 HOH A 197 797 118 HOH HOH . D 4 HOH A 198 798 237 HOH HOH . D 4 HOH A 199 799 193 HOH HOH . D 4 HOH A 200 800 115 HOH HOH . D 4 HOH A 201 801 182 HOH HOH . D 4 HOH A 202 802 64 HOH HOH . D 4 HOH A 203 803 262 HOH HOH . D 4 HOH A 204 804 227 HOH HOH . D 4 HOH A 205 805 110 HOH HOH . D 4 HOH A 206 806 271 HOH HOH . D 4 HOH A 207 807 135 HOH HOH . D 4 HOH A 208 808 122 HOH HOH . D 4 HOH A 209 809 96 HOH HOH . D 4 HOH A 210 810 125 HOH HOH . D 4 HOH A 211 811 196 HOH HOH . D 4 HOH A 212 812 245 HOH HOH . D 4 HOH A 213 813 202 HOH HOH . D 4 HOH A 214 814 253 HOH HOH . D 4 HOH A 215 815 224 HOH HOH . D 4 HOH A 216 816 170 HOH HOH . D 4 HOH A 217 817 254 HOH HOH . D 4 HOH A 218 818 261 HOH HOH . D 4 HOH A 219 819 171 HOH HOH . D 4 HOH A 220 820 239 HOH HOH . D 4 HOH A 221 821 100 HOH HOH . D 4 HOH A 222 822 244 HOH HOH . D 4 HOH A 223 823 228 HOH HOH . D 4 HOH A 224 824 247 HOH HOH . D 4 HOH A 225 825 41 HOH HOH . D 4 HOH A 226 826 273 HOH HOH . D 4 HOH A 227 827 270 HOH HOH . D 4 HOH A 228 828 145 HOH HOH . D 4 HOH A 229 829 93 HOH HOH . D 4 HOH A 230 830 234 HOH HOH . D 4 HOH A 231 831 155 HOH HOH . D 4 HOH A 232 832 91 HOH HOH . D 4 HOH A 233 833 268 HOH HOH . D 4 HOH A 234 834 150 HOH HOH . D 4 HOH A 235 835 154 HOH HOH . D 4 HOH A 236 836 240 HOH HOH . D 4 HOH A 237 837 260 HOH HOH . D 4 HOH A 238 838 142 HOH HOH . D 4 HOH A 239 839 222 HOH HOH . D 4 HOH A 240 840 235 HOH HOH . D 4 HOH A 241 841 209 HOH HOH . D 4 HOH A 242 842 223 HOH HOH . D 4 HOH A 243 843 51 HOH HOH . D 4 HOH A 244 844 197 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 -4.826 20.952 80.954 1 21.74 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 -3.748 20.41 81.499 1 21.13 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 -3.045 20.992 82.451 1 21.87 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 -3.444 22.165 82.886 1 23.38 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 -4.574 22.795 82.36 1 22.59 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 -5.27 22.141 81.351 1 21.97 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 -3.319 19.167 81.093 1 19.63 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 -2.707 22.764 83.877 1 23.11 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 -5.515 20.279 79.847 1 22.04 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 -6.929 19.784 80.171 1 20.79 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 -6.84 18.523 80.68 1 20.91 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 -7.56 19.832 78.757 1 20.81 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 -7.068 20.919 78.18 1 19.96 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 -5.687 21.215 78.926 1 21.43 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 -7.117 18.64 77.974 1 21.03 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 -7.972 22.135 78.354 1 22.41 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 -8.975 22.05 77.379 1 19.03 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 -10.43 22.771 77.695 1 22.14 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 -11.408 22.173 76.73 1 19.3 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 -10.832 22.543 79.13 1 18.6 -1 O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 -10.3 24.386 77.527 1 21.37 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 -9.447 25.227 76.384 1 23.16 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 -9.668 24.575 75.02 1 23.49 -1 O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 -10.041 26.599 76.467 1 21.91 ? O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 -7.983 25.255 76.741 1 23.19 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 507 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #