data_6O88 # _model_server_result.job_id Zhc9KPHAgeYroVu8EcdqUQ _model_server_result.datetime_utc '2025-07-19 03:02:16' _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 6o88 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 6O88 # _exptl.entry_id 6O88 _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 120 _cell.entry_id 6O88 _cell.length_a 98.118 _cell.length_b 98.118 _cell.length_c 91.524 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6O88 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 1 A,B,C,D 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 30.508 # _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 482 n n N1 C6 UDP sing 483 n n N1 C1' UDP sing 484 n n C2 N3 UDP sing 485 n n C2 O2 UDP doub 486 n n N3 C4 UDP sing 487 n n N3 HN3 UDP sing 488 n n C4 C5 UDP sing 489 n n C4 O4 UDP doub 490 n n C5 C6 UDP doub 491 n n C5 H5 UDP sing 492 n n C6 H6 UDP sing 493 n n C1' C2' UDP sing 494 n n C1' O4' UDP sing 495 n n C1' H1' UDP sing 496 n n C2' O2' UDP sing 497 n n C2' C3' UDP sing 498 n n C2' H2' UDP sing 499 n n O2' HO2' UDP sing 500 n n C3' C4' UDP sing 501 n n C3' O3' UDP sing 502 n n C3' H3' UDP sing 503 n n C4' O4' UDP sing 504 n n C4' C5' UDP sing 505 n n C4' H4' UDP sing 506 n n O3' HO3' UDP sing 507 n n C5' O5' UDP sing 508 n n C5' "H5'1" UDP sing 509 n n C5' "H5'2" UDP sing 510 n n O5' PA UDP sing 511 n n PA O1A UDP doub 512 n n PA O2A UDP sing 513 n n PA O3A UDP sing 514 n n O2A HOA2 UDP sing 515 n n O3A PB UDP sing 516 n n PB O1B UDP doub 517 n n PB O2B UDP sing 518 n n PB O3B UDP sing 519 n n O2B HOB2 UDP sing 520 n n O3B HOB3 UDP sing 521 n n # _atom_sites.entry_id 6O88 _atom_sites.fract_transf_matrix[1][1] 0.010192 _atom_sites.fract_transf_matrix[1][2] 0.005884 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011768 _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] 0.010926 _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 1 500 500 UDP UDP . C 3 LRV A 1 501 501 LRV LRV . D 4 HOH A 1 601 601 HOH HOH . D 4 HOH A 2 602 602 HOH HOH . D 4 HOH A 3 603 603 HOH HOH . D 4 HOH A 4 604 604 HOH HOH . D 4 HOH A 5 605 605 HOH HOH . D 4 HOH A 6 606 606 HOH HOH . D 4 HOH A 7 607 607 HOH HOH . D 4 HOH A 8 608 608 HOH HOH . D 4 HOH A 9 609 609 HOH HOH . D 4 HOH A 10 610 610 HOH HOH . D 4 HOH A 11 611 611 HOH HOH . D 4 HOH A 12 612 612 HOH HOH . D 4 HOH A 13 613 613 HOH HOH . D 4 HOH A 14 614 614 HOH HOH . D 4 HOH A 15 615 615 HOH HOH . D 4 HOH A 16 616 616 HOH HOH . D 4 HOH A 17 617 617 HOH HOH . D 4 HOH A 18 618 618 HOH HOH . D 4 HOH A 19 619 619 HOH HOH . D 4 HOH A 20 620 620 HOH HOH . D 4 HOH A 21 621 621 HOH HOH . D 4 HOH A 22 622 622 HOH HOH . D 4 HOH A 23 623 623 HOH HOH . D 4 HOH A 24 624 624 HOH HOH . D 4 HOH A 25 625 625 HOH HOH . D 4 HOH A 26 626 626 HOH HOH . D 4 HOH A 27 627 627 HOH HOH . D 4 HOH A 28 628 628 HOH HOH . D 4 HOH A 29 629 629 HOH HOH . D 4 HOH A 30 630 630 HOH HOH . D 4 HOH A 31 631 631 HOH HOH . D 4 HOH A 32 632 632 HOH HOH . D 4 HOH A 33 633 633 HOH HOH . D 4 HOH A 34 634 634 HOH HOH . D 4 HOH A 35 635 635 HOH HOH . D 4 HOH A 36 636 636 HOH HOH . D 4 HOH A 37 637 637 HOH HOH . D 4 HOH A 38 638 638 HOH HOH . D 4 HOH A 39 639 639 HOH HOH . D 4 HOH A 40 640 640 HOH HOH . D 4 HOH A 41 641 641 HOH HOH . D 4 HOH A 42 642 642 HOH HOH . D 4 HOH A 43 643 643 HOH HOH . D 4 HOH A 44 644 644 HOH HOH . D 4 HOH A 45 645 645 HOH HOH . D 4 HOH A 46 646 646 HOH HOH . D 4 HOH A 47 647 647 HOH HOH . D 4 HOH A 48 648 648 HOH HOH . D 4 HOH A 49 649 649 HOH HOH . D 4 HOH A 50 650 650 HOH HOH . D 4 HOH A 51 651 651 HOH HOH . D 4 HOH A 52 652 652 HOH HOH . D 4 HOH A 53 653 653 HOH HOH . D 4 HOH A 54 654 654 HOH HOH . D 4 HOH A 55 655 655 HOH HOH . D 4 HOH A 56 656 656 HOH HOH . D 4 HOH A 57 657 657 HOH HOH . D 4 HOH A 58 658 658 HOH HOH . D 4 HOH A 59 659 659 HOH HOH . D 4 HOH A 60 660 660 HOH HOH . D 4 HOH A 61 661 661 HOH HOH . D 4 HOH A 62 662 662 HOH HOH . D 4 HOH A 63 663 663 HOH HOH . D 4 HOH A 64 664 664 HOH HOH . D 4 HOH A 65 665 665 HOH HOH . D 4 HOH A 66 666 666 HOH HOH . D 4 HOH A 67 667 667 HOH HOH . D 4 HOH A 68 668 668 HOH HOH . D 4 HOH A 69 669 669 HOH HOH . D 4 HOH A 70 670 670 HOH HOH . D 4 HOH A 71 671 671 HOH HOH . D 4 HOH A 72 672 672 HOH HOH . D 4 HOH A 73 673 673 HOH HOH . D 4 HOH A 74 674 674 HOH HOH . D 4 HOH A 75 675 675 HOH HOH . D 4 HOH A 76 676 676 HOH HOH . D 4 HOH A 77 677 677 HOH HOH . D 4 HOH A 78 678 678 HOH HOH . D 4 HOH A 79 679 679 HOH HOH . D 4 HOH A 80 680 680 HOH HOH . D 4 HOH A 81 681 681 HOH HOH . D 4 HOH A 82 682 682 HOH HOH . D 4 HOH A 83 683 683 HOH HOH . D 4 HOH A 84 684 684 HOH HOH . D 4 HOH A 85 685 685 HOH HOH . D 4 HOH A 86 686 686 HOH HOH . D 4 HOH A 87 687 687 HOH HOH . D 4 HOH A 88 688 688 HOH HOH . D 4 HOH A 89 689 689 HOH HOH . D 4 HOH A 90 690 690 HOH HOH . D 4 HOH A 91 691 691 HOH HOH . D 4 HOH A 92 692 692 HOH HOH . D 4 HOH A 93 693 693 HOH HOH . D 4 HOH A 94 694 694 HOH HOH . D 4 HOH A 95 695 695 HOH HOH . D 4 HOH A 96 696 696 HOH HOH . D 4 HOH A 97 697 697 HOH HOH . D 4 HOH A 98 698 698 HOH HOH . D 4 HOH A 99 699 699 HOH HOH . D 4 HOH A 100 700 700 HOH HOH . D 4 HOH A 101 701 701 HOH HOH . D 4 HOH A 102 702 702 HOH HOH . D 4 HOH A 103 703 703 HOH HOH . D 4 HOH A 104 704 704 HOH HOH . D 4 HOH A 105 705 705 HOH HOH . D 4 HOH A 106 706 706 HOH HOH . D 4 HOH A 107 707 707 HOH HOH . D 4 HOH A 108 708 708 HOH HOH . D 4 HOH A 109 709 709 HOH HOH . D 4 HOH A 110 710 710 HOH HOH . D 4 HOH A 111 711 711 HOH HOH . D 4 HOH A 112 712 712 HOH HOH . D 4 HOH A 113 713 713 HOH HOH . D 4 HOH A 114 714 714 HOH HOH . D 4 HOH A 115 715 715 HOH HOH . D 4 HOH A 116 716 716 HOH HOH . D 4 HOH A 117 717 717 HOH HOH . D 4 HOH A 118 718 718 HOH HOH . D 4 HOH A 119 719 719 HOH HOH . D 4 HOH A 120 720 720 HOH HOH . D 4 HOH A 121 721 721 HOH HOH . D 4 HOH A 122 722 722 HOH HOH . D 4 HOH A 123 723 723 HOH HOH . D 4 HOH A 124 724 724 HOH HOH . D 4 HOH A 125 725 725 HOH HOH . D 4 HOH A 126 726 726 HOH HOH . D 4 HOH A 127 727 727 HOH HOH . D 4 HOH A 128 728 728 HOH HOH . D 4 HOH A 129 729 729 HOH HOH . D 4 HOH A 130 730 730 HOH HOH . D 4 HOH A 131 731 731 HOH HOH . D 4 HOH A 132 732 732 HOH HOH . D 4 HOH A 133 733 733 HOH HOH . D 4 HOH A 134 734 734 HOH HOH . D 4 HOH A 135 735 735 HOH HOH . D 4 HOH A 136 736 736 HOH HOH . D 4 HOH A 137 737 737 HOH HOH . D 4 HOH A 138 738 738 HOH HOH . D 4 HOH A 139 739 739 HOH HOH . D 4 HOH A 140 740 740 HOH HOH . D 4 HOH A 141 741 741 HOH HOH . D 4 HOH A 142 742 742 HOH HOH . D 4 HOH A 143 743 743 HOH HOH . D 4 HOH A 144 744 744 HOH HOH . D 4 HOH A 145 745 745 HOH HOH . D 4 HOH A 146 746 746 HOH HOH . D 4 HOH A 147 747 747 HOH HOH . D 4 HOH A 148 748 748 HOH HOH . D 4 HOH A 149 749 749 HOH HOH . D 4 HOH A 150 750 750 HOH HOH . D 4 HOH A 151 751 751 HOH HOH . D 4 HOH A 152 752 752 HOH HOH . D 4 HOH A 153 753 753 HOH HOH . D 4 HOH A 154 754 754 HOH HOH . D 4 HOH A 155 755 755 HOH HOH . D 4 HOH A 156 756 756 HOH HOH . D 4 HOH A 157 757 757 HOH HOH . D 4 HOH A 158 758 758 HOH HOH . D 4 HOH A 159 759 759 HOH HOH . D 4 HOH A 160 760 760 HOH HOH . D 4 HOH A 161 761 761 HOH HOH . D 4 HOH A 162 762 762 HOH HOH . D 4 HOH A 163 763 763 HOH HOH . D 4 HOH A 164 764 764 HOH HOH . D 4 HOH A 165 765 765 HOH HOH . D 4 HOH A 166 766 766 HOH HOH . D 4 HOH A 167 767 767 HOH HOH . D 4 HOH A 168 768 768 HOH HOH . D 4 HOH A 169 769 769 HOH HOH . D 4 HOH A 170 770 770 HOH HOH . D 4 HOH A 171 771 771 HOH HOH . D 4 HOH A 172 772 772 HOH HOH . D 4 HOH A 173 773 773 HOH HOH . D 4 HOH A 174 774 774 HOH HOH . D 4 HOH A 175 775 775 HOH HOH . D 4 HOH A 176 776 776 HOH HOH . D 4 HOH A 177 777 778 HOH HOH . D 4 HOH A 178 778 779 HOH HOH . D 4 HOH A 179 779 780 HOH HOH . D 4 HOH A 180 780 781 HOH HOH . D 4 HOH A 181 781 782 HOH HOH . D 4 HOH A 182 782 783 HOH HOH . D 4 HOH A 183 783 784 HOH HOH . D 4 HOH A 184 784 785 HOH HOH . D 4 HOH A 185 785 786 HOH HOH . D 4 HOH A 186 786 787 HOH HOH . D 4 HOH A 187 787 788 HOH HOH . D 4 HOH A 188 788 789 HOH HOH . D 4 HOH A 189 789 790 HOH HOH . D 4 HOH A 190 790 791 HOH HOH . D 4 HOH A 191 791 792 HOH HOH . D 4 HOH A 192 792 793 HOH HOH . D 4 HOH A 193 793 794 HOH HOH . D 4 HOH A 194 794 795 HOH HOH . D 4 HOH A 195 795 796 HOH HOH . D 4 HOH A 196 796 797 HOH HOH . D 4 HOH A 197 797 798 HOH HOH . D 4 HOH A 198 798 799 HOH HOH . D 4 HOH A 199 799 800 HOH HOH . D 4 HOH A 200 800 801 HOH HOH . D 4 HOH A 201 801 802 HOH HOH . D 4 HOH A 202 802 803 HOH HOH . D 4 HOH A 203 803 804 HOH HOH . D 4 HOH A 204 804 805 HOH HOH . D 4 HOH A 205 805 806 HOH HOH . D 4 HOH A 206 806 807 HOH HOH . D 4 HOH A 207 807 808 HOH HOH . D 4 HOH A 208 808 809 HOH HOH . D 4 HOH A 209 809 810 HOH HOH . D 4 HOH A 210 810 811 HOH HOH . D 4 HOH A 211 811 812 HOH HOH . D 4 HOH A 212 812 814 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 16.257 -15.085 2.701 1 27.1 ? N1 UDP 500 A 1 HETATM 2 C C2 UDP . . . B 2 15.572 -14.579 3.784 1 26.25 ? C2 UDP 500 A 1 HETATM 3 N N3 UDP . . . B 2 14.259 -14.198 3.659 1 21.9 ? N3 UDP 500 A 1 HETATM 4 C C4 UDP . . . B 2 13.645 -14.322 2.427 1 26.67 ? C4 UDP 500 A 1 HETATM 5 C C5 UDP . . . B 2 14.331 -14.844 1.326 1 22.48 ? C5 UDP 500 A 1 HETATM 6 C C6 UDP . . . B 2 15.62 -15.334 1.52 1 22.59 ? C6 UDP 500 A 1 HETATM 7 O O2 UDP . . . B 2 16.152 -14.477 4.858 1 23.92 ? O2 UDP 500 A 1 HETATM 8 O O4 UDP . . . B 2 12.474 -13.98 2.315 1 26.28 ? O4 UDP 500 A 1 HETATM 9 C C1' UDP . . . B 2 17.662 -15.465 2.914 1 19.93 ? C1' UDP 500 A 1 HETATM 10 C C2' UDP . . . B 2 17.82 -16.985 2.856 1 23.17 ? C2' UDP 500 A 1 HETATM 11 O O2' UDP . . . B 2 17.578 -17.624 4.103 1 26.81 ? O2' UDP 500 A 1 HETATM 12 C C3' UDP . . . B 2 19.249 -17.094 2.332 1 21.82 ? C3' UDP 500 A 1 HETATM 13 C C4' UDP . . . B 2 19.479 -15.829 1.493 1 21.29 ? C4' UDP 500 A 1 HETATM 14 O O4' UDP . . . B 2 18.437 -14.932 1.854 1 23.34 ? O4' UDP 500 A 1 HETATM 15 O O3' UDP . . . B 2 20.173 -17.098 3.385 1 21.9 ? O3' UDP 500 A 1 HETATM 16 C C5' UDP . . . B 2 19.431 -16.132 -0.014 1 24.19 ? C5' UDP 500 A 1 HETATM 17 O O5' UDP . . . B 2 20.648 -16.725 -0.417 1 22.57 ? O5' UDP 500 A 1 HETATM 18 P PA UDP . . . B 2 20.722 -17.753 -1.66 1 26.13 ? PA UDP 500 A 1 HETATM 19 O O1A UDP . . . B 2 22.099 -18.297 -1.664 1 26.22 ? O1A UDP 500 A 1 HETATM 20 O O2A UDP . . . B 2 19.718 -18.83 -1.492 1 27.7 ? O2A UDP 500 A 1 HETATM 21 O O3A UDP . . . B 2 20.201 -16.982 -2.954 1 31.94 ? O3A UDP 500 A 1 HETATM 22 P PB UDP . . . B 2 20.655 -15.559 -3.557 1 32.03 ? PB UDP 500 A 1 HETATM 23 O O1B UDP . . . B 2 20.502 -15.767 -5.009 1 30.94 ? O1B UDP 500 A 1 HETATM 24 O O2B UDP . . . B 2 19.712 -14.552 -3.042 1 28.94 ? O2B UDP 500 A 1 HETATM 25 O O3B UDP . . . B 2 22.037 -15.22 -3.191 1 37.69 ? O3B UDP 500 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #