data_8INV # _model_server_result.job_id gbg3KWJ5xdcfaAKX4L0Apg _model_server_result.datetime_utc '2024-11-28 19:14:06' _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 8inv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8INV # _exptl.entry_id 8INV _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 8INV _cell.length_a 45.682 _cell.length_b 52.281 _cell.length_c 200.852 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8INV _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,E _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 443 n n N1 C6 UDP sing 444 n n N1 C1' UDP sing 445 n n C2 N3 UDP sing 446 n n C2 O2 UDP doub 447 n n N3 C4 UDP sing 448 n n N3 HN3 UDP sing 449 n n C4 C5 UDP sing 450 n n C4 O4 UDP doub 451 n n C5 C6 UDP doub 452 n n C5 H5 UDP sing 453 n n C6 H6 UDP sing 454 n n C1' C2' UDP sing 455 n n C1' O4' UDP sing 456 n n C1' H1' UDP sing 457 n n C2' O2' UDP sing 458 n n C2' C3' UDP sing 459 n n C2' H2' UDP sing 460 n n O2' HO2' UDP sing 461 n n C3' C4' UDP sing 462 n n C3' O3' UDP sing 463 n n C3' H3' UDP sing 464 n n C4' O4' UDP sing 465 n n C4' C5' UDP sing 466 n n C4' H4' UDP sing 467 n n O3' HO3' UDP sing 468 n n C5' O5' UDP sing 469 n n C5' "H5'1" UDP sing 470 n n C5' "H5'2" UDP sing 471 n n O5' PA UDP sing 472 n n PA O1A UDP doub 473 n n PA O2A UDP sing 474 n n PA O3A UDP sing 475 n n O2A HOA2 UDP sing 476 n n O3A PB UDP sing 477 n n PB O1B UDP doub 478 n n PB O2B UDP sing 479 n n PB O3B UDP sing 480 n n O2B HOB2 UDP sing 481 n n O3B HOB3 UDP sing 482 n n # _atom_sites.entry_id 8INV _atom_sites.fract_transf_matrix[1][1] 0.02189 _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] 0.019127 _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] 0.004979 _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 1 501 502 UDP UDP . C 3 TRS A 1 502 503 TRS TRS . D 4 BUF A 1 503 504 BUF DRG . E 5 HOH A 1 601 153 HOH HOH . E 5 HOH A 2 602 59 HOH HOH . E 5 HOH A 3 603 221 HOH HOH . E 5 HOH A 4 604 214 HOH HOH . E 5 HOH A 5 605 103 HOH HOH . E 5 HOH A 6 606 143 HOH HOH . E 5 HOH A 7 607 167 HOH HOH . E 5 HOH A 8 608 28 HOH HOH . E 5 HOH A 9 609 176 HOH HOH . E 5 HOH A 10 610 142 HOH HOH . E 5 HOH A 11 611 34 HOH HOH . E 5 HOH A 12 612 67 HOH HOH . E 5 HOH A 13 613 16 HOH HOH . E 5 HOH A 14 614 105 HOH HOH . E 5 HOH A 15 615 42 HOH HOH . E 5 HOH A 16 616 207 HOH HOH . E 5 HOH A 17 617 73 HOH HOH . E 5 HOH A 18 618 110 HOH HOH . E 5 HOH A 19 619 45 HOH HOH . E 5 HOH A 20 620 22 HOH HOH . E 5 HOH A 21 621 173 HOH HOH . E 5 HOH A 22 622 31 HOH HOH . E 5 HOH A 23 623 236 HOH HOH . E 5 HOH A 24 624 27 HOH HOH . E 5 HOH A 25 625 1 HOH HOH . E 5 HOH A 26 626 39 HOH HOH . E 5 HOH A 27 627 254 HOH HOH . E 5 HOH A 28 628 193 HOH HOH . E 5 HOH A 29 629 9 HOH HOH . E 5 HOH A 30 630 135 HOH HOH . E 5 HOH A 31 631 160 HOH HOH . E 5 HOH A 32 632 18 HOH HOH . E 5 HOH A 33 633 3 HOH HOH . E 5 HOH A 34 634 70 HOH HOH . E 5 HOH A 35 635 91 HOH HOH . E 5 HOH A 36 636 25 HOH HOH . E 5 HOH A 37 637 13 HOH HOH . E 5 HOH A 38 638 14 HOH HOH . E 5 HOH A 39 639 107 HOH HOH . E 5 HOH A 40 640 106 HOH HOH . E 5 HOH A 41 641 7 HOH HOH . E 5 HOH A 42 642 140 HOH HOH . E 5 HOH A 43 643 146 HOH HOH . E 5 HOH A 44 644 24 HOH HOH . E 5 HOH A 45 645 102 HOH HOH . E 5 HOH A 46 646 2 HOH HOH . E 5 HOH A 47 647 61 HOH HOH . E 5 HOH A 48 648 48 HOH HOH . E 5 HOH A 49 649 228 HOH HOH . E 5 HOH A 50 650 38 HOH HOH . E 5 HOH A 51 651 15 HOH HOH . E 5 HOH A 52 652 244 HOH HOH . E 5 HOH A 53 653 192 HOH HOH . E 5 HOH A 54 654 154 HOH HOH . E 5 HOH A 55 655 183 HOH HOH . E 5 HOH A 56 656 78 HOH HOH . E 5 HOH A 57 657 161 HOH HOH . E 5 HOH A 58 658 4 HOH HOH . E 5 HOH A 59 659 52 HOH HOH . E 5 HOH A 60 660 132 HOH HOH . E 5 HOH A 61 661 163 HOH HOH . E 5 HOH A 62 662 5 HOH HOH . E 5 HOH A 63 663 20 HOH HOH . E 5 HOH A 64 664 79 HOH HOH . E 5 HOH A 65 665 128 HOH HOH . E 5 HOH A 66 666 81 HOH HOH . E 5 HOH A 67 667 126 HOH HOH . E 5 HOH A 68 668 98 HOH HOH . E 5 HOH A 69 669 65 HOH HOH . E 5 HOH A 70 670 47 HOH HOH . E 5 HOH A 71 671 37 HOH HOH . E 5 HOH A 72 672 200 HOH HOH . E 5 HOH A 73 673 54 HOH HOH . E 5 HOH A 74 674 8 HOH HOH . E 5 HOH A 75 675 62 HOH HOH . E 5 HOH A 76 676 147 HOH HOH . E 5 HOH A 77 677 19 HOH HOH . E 5 HOH A 78 678 87 HOH HOH . E 5 HOH A 79 679 184 HOH HOH . E 5 HOH A 80 680 124 HOH HOH . E 5 HOH A 81 681 11 HOH HOH . E 5 HOH A 82 682 100 HOH HOH . E 5 HOH A 83 683 109 HOH HOH . E 5 HOH A 84 684 6 HOH HOH . E 5 HOH A 85 685 30 HOH HOH . E 5 HOH A 86 686 169 HOH HOH . E 5 HOH A 87 687 58 HOH HOH . E 5 HOH A 88 688 111 HOH HOH . E 5 HOH A 89 689 43 HOH HOH . E 5 HOH A 90 690 177 HOH HOH . E 5 HOH A 91 691 114 HOH HOH . E 5 HOH A 92 692 158 HOH HOH . E 5 HOH A 93 693 26 HOH HOH . E 5 HOH A 94 694 134 HOH HOH . E 5 HOH A 95 695 149 HOH HOH . E 5 HOH A 96 696 56 HOH HOH . E 5 HOH A 97 697 99 HOH HOH . E 5 HOH A 98 698 33 HOH HOH . E 5 HOH A 99 699 101 HOH HOH . E 5 HOH A 100 700 238 HOH HOH . E 5 HOH A 101 701 152 HOH HOH . E 5 HOH A 102 702 112 HOH HOH . E 5 HOH A 103 703 93 HOH HOH . E 5 HOH A 104 704 75 HOH HOH . E 5 HOH A 105 705 68 HOH HOH . E 5 HOH A 106 706 196 HOH HOH . E 5 HOH A 107 707 72 HOH HOH . E 5 HOH A 108 708 233 HOH HOH . E 5 HOH A 109 709 104 HOH HOH . E 5 HOH A 110 710 189 HOH HOH . E 5 HOH A 111 711 92 HOH HOH . E 5 HOH A 112 712 113 HOH HOH . E 5 HOH A 113 713 57 HOH HOH . E 5 HOH A 114 714 84 HOH HOH . E 5 HOH A 115 715 32 HOH HOH . E 5 HOH A 116 716 96 HOH HOH . E 5 HOH A 117 717 35 HOH HOH . E 5 HOH A 118 718 122 HOH HOH . E 5 HOH A 119 719 71 HOH HOH . E 5 HOH A 120 720 159 HOH HOH . E 5 HOH A 121 721 211 HOH HOH . E 5 HOH A 122 722 12 HOH HOH . E 5 HOH A 123 723 63 HOH HOH . E 5 HOH A 124 724 197 HOH HOH . E 5 HOH A 125 725 60 HOH HOH . E 5 HOH A 126 726 89 HOH HOH . E 5 HOH A 127 727 29 HOH HOH . E 5 HOH A 128 728 118 HOH HOH . E 5 HOH A 129 729 85 HOH HOH . E 5 HOH A 130 730 76 HOH HOH . E 5 HOH A 131 731 250 HOH HOH . E 5 HOH A 132 732 82 HOH HOH . E 5 HOH A 133 733 137 HOH HOH . E 5 HOH A 134 734 46 HOH HOH . E 5 HOH A 135 735 64 HOH HOH . E 5 HOH A 136 736 253 HOH HOH . E 5 HOH A 137 737 230 HOH HOH . E 5 HOH A 138 738 86 HOH HOH . E 5 HOH A 139 739 123 HOH HOH . E 5 HOH A 140 740 239 HOH HOH . E 5 HOH A 141 741 125 HOH HOH . E 5 HOH A 142 742 150 HOH HOH . E 5 HOH A 143 743 129 HOH HOH . E 5 HOH A 144 744 208 HOH HOH . E 5 HOH A 145 745 55 HOH HOH . E 5 HOH A 146 746 95 HOH HOH . E 5 HOH A 147 747 36 HOH HOH . E 5 HOH A 148 748 187 HOH HOH . E 5 HOH A 149 749 138 HOH HOH . E 5 HOH A 150 750 246 HOH HOH . E 5 HOH A 151 751 117 HOH HOH . E 5 HOH A 152 752 195 HOH HOH . E 5 HOH A 153 753 242 HOH HOH . E 5 HOH A 154 754 21 HOH HOH . E 5 HOH A 155 755 88 HOH HOH . E 5 HOH A 156 756 219 HOH HOH . E 5 HOH A 157 757 53 HOH HOH . E 5 HOH A 158 758 97 HOH HOH . E 5 HOH A 159 759 80 HOH HOH . E 5 HOH A 160 760 255 HOH HOH . E 5 HOH A 161 761 23 HOH HOH . E 5 HOH A 162 762 10 HOH HOH . E 5 HOH A 163 763 133 HOH HOH . E 5 HOH A 164 764 166 HOH HOH . E 5 HOH A 165 765 226 HOH HOH . E 5 HOH A 166 766 180 HOH HOH . E 5 HOH A 167 767 17 HOH HOH . E 5 HOH A 168 768 156 HOH HOH . E 5 HOH A 169 769 136 HOH HOH . E 5 HOH A 170 770 127 HOH HOH . E 5 HOH A 171 771 215 HOH HOH . E 5 HOH A 172 772 190 HOH HOH . E 5 HOH A 173 773 77 HOH HOH . E 5 HOH A 174 774 178 HOH HOH . E 5 HOH A 175 775 40 HOH HOH . E 5 HOH A 176 776 243 HOH HOH . E 5 HOH A 177 777 145 HOH HOH . E 5 HOH A 178 778 257 HOH HOH . E 5 HOH A 179 779 115 HOH HOH . E 5 HOH A 180 780 74 HOH HOH . E 5 HOH A 181 781 204 HOH HOH . E 5 HOH A 182 782 198 HOH HOH . E 5 HOH A 183 783 69 HOH HOH . E 5 HOH A 184 784 94 HOH HOH . E 5 HOH A 185 785 256 HOH HOH . E 5 HOH A 186 786 205 HOH HOH . E 5 HOH A 187 787 108 HOH HOH . E 5 HOH A 188 788 241 HOH HOH . E 5 HOH A 189 789 220 HOH HOH . E 5 HOH A 190 790 206 HOH HOH . E 5 HOH A 191 791 223 HOH HOH . E 5 HOH A 192 792 194 HOH HOH . E 5 HOH A 193 793 155 HOH HOH . E 5 HOH A 194 794 217 HOH HOH . E 5 HOH A 195 795 185 HOH HOH . E 5 HOH A 196 796 66 HOH HOH . E 5 HOH A 197 797 224 HOH HOH . E 5 HOH A 198 798 191 HOH HOH . E 5 HOH A 199 799 148 HOH HOH . E 5 HOH A 200 800 251 HOH HOH . E 5 HOH A 201 801 248 HOH HOH . E 5 HOH A 202 802 171 HOH HOH . E 5 HOH A 203 803 172 HOH HOH . E 5 HOH A 204 804 116 HOH HOH . E 5 HOH A 205 805 119 HOH HOH . E 5 HOH A 206 806 51 HOH HOH . E 5 HOH A 207 807 170 HOH HOH . E 5 HOH A 208 808 240 HOH HOH . E 5 HOH A 209 809 165 HOH HOH . E 5 HOH A 210 810 188 HOH HOH . E 5 HOH A 211 811 130 HOH HOH . E 5 HOH A 212 812 174 HOH HOH . E 5 HOH A 213 813 222 HOH HOH . E 5 HOH A 214 814 231 HOH HOH . E 5 HOH A 215 815 218 HOH HOH . E 5 HOH A 216 816 203 HOH HOH . E 5 HOH A 217 817 212 HOH HOH . E 5 HOH A 218 818 227 HOH HOH . E 5 HOH A 219 819 139 HOH HOH . E 5 HOH A 220 820 213 HOH HOH . E 5 HOH A 221 821 141 HOH HOH . E 5 HOH A 222 822 209 HOH HOH . E 5 HOH A 223 823 164 HOH HOH . E 5 HOH A 224 824 247 HOH HOH . E 5 HOH A 225 825 234 HOH HOH . E 5 HOH A 226 826 121 HOH HOH . E 5 HOH A 227 827 235 HOH HOH . E 5 HOH A 228 828 201 HOH HOH . E 5 HOH A 229 829 225 HOH HOH . E 5 HOH A 230 830 162 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 -4.551 20.878 80.501 1 20.64 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 -3.453 20.348 81.007 1 20.44 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 -2.769 20.922 81.973 1 20.83 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 -3.18 22.087 82.43 1 20.24 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 -4.326 22.707 81.928 1 22.06 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 -5.017 22.047 80.923 1 20.75 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 -3.028 19.112 80.54 1 19.66 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 -2.444 22.684 83.429 1 22.2 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 -5.231 20.19 79.388 1 20.98 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 -6.636 19.681 79.695 1 21.11 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 -6.514 18.412 80.18 1 21.4 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 -7.262 19.754 78.278 1 20.66 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 -6.758 20.825 77.694 1 17.96 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 -5.375 21.096 78.436 1 20.33 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 -6.809 18.576 77.48 1 22.58 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 -7.638 22.061 77.861 1 18.89 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 -8.699 21.871 76.966 1 17.93 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 -10.133 22.619 77.203 1 19.73 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 -11.134 22.062 76.221 1 18.61 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 -10.597 22.437 78.655 1 17.65 -1 O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 -9.94 24.23 77.061 1 19.87 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 -9.073 25.099 75.963 1 21.21 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 -9.291 24.451 74.6 1 19.02 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 -9.708 26.457 76.004 1 19.82 -1 O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 -7.605 25.129 76.348 1 20.03 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 43 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 25 #