data_6INF # _model_server_result.job_id 6J-NlK60fWgXuaK3Qui1aA _model_server_result.datetime_utc '2025-07-20 11:11:44' _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 6inf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6INF # _exptl.entry_id 6INF _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 6INF _cell.length_a 97.662 _cell.length_b 97.662 _cell.length_c 89.626 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6INF _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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 358 n n N1 C6 UDP sing 359 n n N1 C1' UDP sing 360 n n C2 N3 UDP sing 361 n n C2 O2 UDP doub 362 n n N3 C4 UDP sing 363 n n N3 HN3 UDP sing 364 n n C4 C5 UDP sing 365 n n C4 O4 UDP doub 366 n n C5 C6 UDP doub 367 n n C5 H5 UDP sing 368 n n C6 H6 UDP sing 369 n n C1' C2' UDP sing 370 n n C1' O4' UDP sing 371 n n C1' H1' UDP sing 372 n n C2' O2' UDP sing 373 n n C2' C3' UDP sing 374 n n C2' H2' UDP sing 375 n n O2' HO2' UDP sing 376 n n C3' C4' UDP sing 377 n n C3' O3' UDP sing 378 n n C3' H3' UDP sing 379 n n C4' O4' UDP sing 380 n n C4' C5' UDP sing 381 n n C4' H4' UDP sing 382 n n O3' HO3' UDP sing 383 n n C5' O5' UDP sing 384 n n C5' "H5'1" UDP sing 385 n n C5' "H5'2" UDP sing 386 n n O5' PA UDP sing 387 n n PA O1A UDP doub 388 n n PA O2A UDP sing 389 n n PA O3A UDP sing 390 n n O2A HOA2 UDP sing 391 n n O3A PB UDP sing 392 n n PB O1B UDP doub 393 n n PB O2B UDP sing 394 n n PB O3B UDP sing 395 n n O2B HOB2 UDP sing 396 n n O3B HOB3 UDP sing 397 n n # _atom_sites.entry_id 6INF _atom_sites.fract_transf_matrix[1][1] 0.010239 _atom_sites.fract_transf_matrix[1][2] 0.005912 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011823 _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] 0.011157 _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 2 UDP UDP . C 3 HOH A 1 601 84 HOH HOH . C 3 HOH A 2 602 86 HOH HOH . C 3 HOH A 3 603 127 HOH HOH . C 3 HOH A 4 604 149 HOH HOH . C 3 HOH A 5 605 40 HOH HOH . C 3 HOH A 6 606 158 HOH HOH . C 3 HOH A 7 607 50 HOH HOH . C 3 HOH A 8 608 33 HOH HOH . C 3 HOH A 9 609 135 HOH HOH . C 3 HOH A 10 610 159 HOH HOH . C 3 HOH A 11 611 34 HOH HOH . C 3 HOH A 12 612 72 HOH HOH . C 3 HOH A 13 613 48 HOH HOH . C 3 HOH A 14 614 152 HOH HOH . C 3 HOH A 15 615 12 HOH HOH . C 3 HOH A 16 616 170 HOH HOH . C 3 HOH A 17 617 154 HOH HOH . C 3 HOH A 18 618 110 HOH HOH . C 3 HOH A 19 619 167 HOH HOH . C 3 HOH A 20 620 24 HOH HOH . C 3 HOH A 21 621 184 HOH HOH . C 3 HOH A 22 622 37 HOH HOH . C 3 HOH A 23 623 43 HOH HOH . C 3 HOH A 24 624 139 HOH HOH . C 3 HOH A 25 625 5 HOH HOH . C 3 HOH A 26 626 69 HOH HOH . C 3 HOH A 27 627 111 HOH HOH . C 3 HOH A 28 628 42 HOH HOH . C 3 HOH A 29 629 161 HOH HOH . C 3 HOH A 30 630 121 HOH HOH . C 3 HOH A 31 631 163 HOH HOH . C 3 HOH A 32 632 1 HOH HOH . C 3 HOH A 33 633 128 HOH HOH . C 3 HOH A 34 634 8 HOH HOH . C 3 HOH A 35 635 63 HOH HOH . C 3 HOH A 36 636 44 HOH HOH . C 3 HOH A 37 637 104 HOH HOH . C 3 HOH A 38 638 120 HOH HOH . C 3 HOH A 39 639 77 HOH HOH . C 3 HOH A 40 640 193 HOH HOH . C 3 HOH A 41 641 131 HOH HOH . C 3 HOH A 42 642 52 HOH HOH . C 3 HOH A 43 643 171 HOH HOH . C 3 HOH A 44 644 76 HOH HOH . C 3 HOH A 45 645 45 HOH HOH . C 3 HOH A 46 646 55 HOH HOH . C 3 HOH A 47 647 177 HOH HOH . C 3 HOH A 48 648 164 HOH HOH . C 3 HOH A 49 649 47 HOH HOH . C 3 HOH A 50 650 68 HOH HOH . C 3 HOH A 51 651 41 HOH HOH . C 3 HOH A 52 652 27 HOH HOH . C 3 HOH A 53 653 3 HOH HOH . C 3 HOH A 54 654 108 HOH HOH . C 3 HOH A 55 655 11 HOH HOH . C 3 HOH A 56 656 145 HOH HOH . C 3 HOH A 57 657 51 HOH HOH . C 3 HOH A 58 658 106 HOH HOH . C 3 HOH A 59 659 191 HOH HOH . C 3 HOH A 60 660 105 HOH HOH . C 3 HOH A 61 661 4 HOH HOH . C 3 HOH A 62 662 112 HOH HOH . C 3 HOH A 63 663 61 HOH HOH . C 3 HOH A 64 664 117 HOH HOH . C 3 HOH A 65 665 35 HOH HOH . C 3 HOH A 66 666 95 HOH HOH . C 3 HOH A 67 667 39 HOH HOH . C 3 HOH A 68 668 144 HOH HOH . C 3 HOH A 69 669 98 HOH HOH . C 3 HOH A 70 670 93 HOH HOH . C 3 HOH A 71 671 25 HOH HOH . C 3 HOH A 72 672 115 HOH HOH . C 3 HOH A 73 673 82 HOH HOH . C 3 HOH A 74 674 103 HOH HOH . C 3 HOH A 75 675 99 HOH HOH . C 3 HOH A 76 676 123 HOH HOH . C 3 HOH A 77 677 67 HOH HOH . C 3 HOH A 78 678 134 HOH HOH . C 3 HOH A 79 679 178 HOH HOH . C 3 HOH A 80 680 18 HOH HOH . C 3 HOH A 81 681 59 HOH HOH . C 3 HOH A 82 682 172 HOH HOH . C 3 HOH A 83 683 132 HOH HOH . C 3 HOH A 84 684 56 HOH HOH . C 3 HOH A 85 685 122 HOH HOH . C 3 HOH A 86 686 141 HOH HOH . C 3 HOH A 87 687 188 HOH HOH . C 3 HOH A 88 688 31 HOH HOH . C 3 HOH A 89 689 10 HOH HOH . C 3 HOH A 90 690 192 HOH HOH . C 3 HOH A 91 691 30 HOH HOH . C 3 HOH A 92 692 29 HOH HOH . C 3 HOH A 93 693 133 HOH HOH . C 3 HOH A 94 694 49 HOH HOH . C 3 HOH A 95 695 53 HOH HOH . C 3 HOH A 96 696 9 HOH HOH . C 3 HOH A 97 697 83 HOH HOH . C 3 HOH A 98 698 97 HOH HOH . C 3 HOH A 99 699 96 HOH HOH . C 3 HOH A 100 700 124 HOH HOH . C 3 HOH A 101 701 87 HOH HOH . C 3 HOH A 102 702 101 HOH HOH . C 3 HOH A 103 703 2 HOH HOH . C 3 HOH A 104 704 187 HOH HOH . C 3 HOH A 105 705 21 HOH HOH . C 3 HOH A 106 706 166 HOH HOH . C 3 HOH A 107 707 15 HOH HOH . C 3 HOH A 108 708 109 HOH HOH . C 3 HOH A 109 709 7 HOH HOH . C 3 HOH A 110 710 180 HOH HOH . C 3 HOH A 111 711 13 HOH HOH . C 3 HOH A 112 712 70 HOH HOH . C 3 HOH A 113 713 186 HOH HOH . C 3 HOH A 114 714 54 HOH HOH . C 3 HOH A 115 715 142 HOH HOH . C 3 HOH A 116 716 160 HOH HOH . C 3 HOH A 117 717 153 HOH HOH . C 3 HOH A 118 718 19 HOH HOH . C 3 HOH A 119 719 14 HOH HOH . C 3 HOH A 120 720 46 HOH HOH . C 3 HOH A 121 721 28 HOH HOH . C 3 HOH A 122 722 185 HOH HOH . C 3 HOH A 123 723 94 HOH HOH . C 3 HOH A 124 724 57 HOH HOH . C 3 HOH A 125 725 157 HOH HOH . C 3 HOH A 126 726 181 HOH HOH . C 3 HOH A 127 727 36 HOH HOH . C 3 HOH A 128 728 6 HOH HOH . C 3 HOH A 129 729 74 HOH HOH . C 3 HOH A 130 730 60 HOH HOH . C 3 HOH A 131 731 125 HOH HOH . C 3 HOH A 132 732 179 HOH HOH . C 3 HOH A 133 733 116 HOH HOH . C 3 HOH A 134 734 168 HOH HOH . C 3 HOH A 135 735 143 HOH HOH . C 3 HOH A 136 736 71 HOH HOH . C 3 HOH A 137 737 32 HOH HOH . C 3 HOH A 138 738 126 HOH HOH . C 3 HOH A 139 739 90 HOH HOH . C 3 HOH A 140 740 190 HOH HOH . C 3 HOH A 141 741 119 HOH HOH . C 3 HOH A 142 742 16 HOH HOH . C 3 HOH A 143 743 176 HOH HOH . C 3 HOH A 144 744 65 HOH HOH . C 3 HOH A 145 745 155 HOH HOH . C 3 HOH A 146 746 102 HOH HOH . C 3 HOH A 147 747 17 HOH HOH . C 3 HOH A 148 748 91 HOH HOH . C 3 HOH A 149 749 23 HOH HOH . C 3 HOH A 150 750 129 HOH HOH . C 3 HOH A 151 751 80 HOH HOH . C 3 HOH A 152 752 26 HOH HOH . C 3 HOH A 153 753 66 HOH HOH . C 3 HOH A 154 754 89 HOH HOH . C 3 HOH A 155 755 194 HOH HOH . C 3 HOH A 156 756 38 HOH HOH . C 3 HOH A 157 757 150 HOH HOH . C 3 HOH A 158 758 183 HOH HOH . C 3 HOH A 159 759 140 HOH HOH . C 3 HOH A 160 760 113 HOH HOH . C 3 HOH A 161 761 62 HOH HOH . C 3 HOH A 162 762 88 HOH HOH . C 3 HOH A 163 763 118 HOH HOH . C 3 HOH A 164 764 79 HOH HOH . C 3 HOH A 165 765 165 HOH HOH . C 3 HOH A 166 766 136 HOH HOH . C 3 HOH A 167 767 169 HOH HOH . C 3 HOH A 168 768 175 HOH HOH . C 3 HOH A 169 769 189 HOH HOH . C 3 HOH A 170 770 81 HOH HOH . C 3 HOH A 171 771 73 HOH HOH . C 3 HOH A 172 772 58 HOH HOH . C 3 HOH A 173 773 148 HOH HOH . C 3 HOH A 174 774 114 HOH HOH . C 3 HOH A 175 775 75 HOH HOH . C 3 HOH A 176 776 85 HOH HOH . C 3 HOH A 177 777 174 HOH HOH . C 3 HOH A 178 778 100 HOH HOH . C 3 HOH A 179 779 146 HOH HOH . C 3 HOH A 180 780 151 HOH HOH . C 3 HOH A 181 781 92 HOH HOH . C 3 HOH A 182 782 162 HOH HOH . C 3 HOH A 183 783 107 HOH HOH . C 3 HOH A 184 784 182 HOH HOH . C 3 HOH A 185 785 147 HOH HOH . C 3 HOH A 186 786 138 HOH HOH . C 3 HOH A 187 787 64 HOH HOH . C 3 HOH A 188 788 156 HOH HOH . C 3 HOH A 189 789 173 HOH HOH . C 3 HOH A 190 790 130 HOH HOH . C 3 HOH A 191 791 137 HOH HOH . C 3 HOH A 192 792 78 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 16.319 -14.86 2.296 1 20.95 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 15.569 -14.444 3.416 1 19.93 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 14.286 -14.135 3.242 1 21.24 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 13.68 -14.192 2.061 1 20.83 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 14.381 -14.63 0.929 1 22.04 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 15.73 -14.944 1.096 1 19.56 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 16.095 -14.371 4.544 1 23.2 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 12.468 -13.889 1.959 1 23.75 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 17.713 -15.209 2.476 1 21.97 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 17.932 -16.715 2.36 1 19.21 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 17.69 -17.36 3.61 1 23.04 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 19.387 -16.75 1.966 1 18.63 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 19.584 -15.484 1.133 1 21.63 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 18.502 -14.617 1.451 1 23.41 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 20.23 -16.74 3.092 1 19.75 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 19.5 -15.759 -0.357 1 20.48 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 20.68 -16.448 -0.743 1 24.37 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 20.741 -17.458 -1.973 1 24.06 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 22.136 -17.945 -2.024 1 21.76 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 19.683 -18.511 -1.803 1 25.86 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 20.307 -16.802 -3.357 1 28.22 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 20.254 -15.318 -3.99 1 28.64 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 20.255 -15.677 -5.455 1 24.04 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 21.436 -14.575 -3.458 1 33.06 ? O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 18.898 -14.796 -3.583 1 30.14 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #