data_6INH # _model_server_result.job_id B5z5ZO9YN0X3SSyuVJqefQ _model_server_result.datetime_utc '2025-07-20 16:53:53' _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 6inh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6INH # _exptl.entry_id 6INH _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 6INH _cell.length_a 97.553 _cell.length_b 97.553 _cell.length_c 90.774 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6INH _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,D,E,F,G _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 471 n n N1 C6 UDP sing 472 n n N1 C1' UDP sing 473 n n C2 N3 UDP sing 474 n n C2 O2 UDP doub 475 n n N3 C4 UDP sing 476 n n N3 HN3 UDP sing 477 n n C4 C5 UDP sing 478 n n C4 O4 UDP doub 479 n n C5 C6 UDP doub 480 n n C5 H5 UDP sing 481 n n C6 H6 UDP sing 482 n n C1' C2' UDP sing 483 n n C1' O4' UDP sing 484 n n C1' H1' UDP sing 485 n n C2' O2' UDP sing 486 n n C2' C3' UDP sing 487 n n C2' H2' UDP sing 488 n n O2' HO2' UDP sing 489 n n C3' C4' UDP sing 490 n n C3' O3' UDP sing 491 n n C3' H3' UDP sing 492 n n C4' O4' UDP sing 493 n n C4' C5' UDP sing 494 n n C4' H4' UDP sing 495 n n O3' HO3' UDP sing 496 n n C5' O5' UDP sing 497 n n C5' "H5'1" UDP sing 498 n n C5' "H5'2" UDP sing 499 n n O5' PA UDP sing 500 n n PA O1A UDP doub 501 n n PA O2A UDP sing 502 n n PA O3A UDP sing 503 n n O2A HOA2 UDP sing 504 n n O3A PB UDP sing 505 n n PB O1B UDP doub 506 n n PB O2B UDP sing 507 n n PB O3B UDP sing 508 n n O2B HOB2 UDP sing 509 n n O3B HOB3 UDP sing 510 n n # _atom_sites.entry_id 6INH _atom_sites.fract_transf_matrix[1][1] 0.010251 _atom_sites.fract_transf_matrix[1][2] 0.005918 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011837 _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] 0.011016 _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 AQ9 A 1 502 1 AQ9 RUB . D 4 GOL A 1 503 1 GOL GOL . E 4 GOL A 1 504 2 GOL GOL . F 3 AQ9 A 1 505 1 AQ9 2RU . G 5 HOH A 1 601 131 HOH HOH . G 5 HOH A 2 602 60 HOH HOH . G 5 HOH A 3 603 95 HOH HOH . G 5 HOH A 4 604 156 HOH HOH . G 5 HOH A 5 605 62 HOH HOH . G 5 HOH A 6 606 183 HOH HOH . G 5 HOH A 7 607 130 HOH HOH . G 5 HOH A 8 608 138 HOH HOH . G 5 HOH A 9 609 164 HOH HOH . G 5 HOH A 10 610 113 HOH HOH . G 5 HOH A 11 611 158 HOH HOH . G 5 HOH A 12 612 74 HOH HOH . G 5 HOH A 13 613 107 HOH HOH . G 5 HOH A 14 614 217 HOH HOH . G 5 HOH A 15 615 35 HOH HOH . G 5 HOH A 16 616 66 HOH HOH . G 5 HOH A 17 617 222 HOH HOH . G 5 HOH A 18 618 167 HOH HOH . G 5 HOH A 19 619 58 HOH HOH . G 5 HOH A 20 620 88 HOH HOH . G 5 HOH A 21 621 64 HOH HOH . G 5 HOH A 22 622 172 HOH HOH . G 5 HOH A 23 623 162 HOH HOH . G 5 HOH A 24 624 191 HOH HOH . G 5 HOH A 25 625 55 HOH HOH . G 5 HOH A 26 626 28 HOH HOH . G 5 HOH A 27 627 163 HOH HOH . G 5 HOH A 28 628 84 HOH HOH . G 5 HOH A 29 629 96 HOH HOH . G 5 HOH A 30 630 50 HOH HOH . G 5 HOH A 31 631 34 HOH HOH . G 5 HOH A 32 632 69 HOH HOH . G 5 HOH A 33 633 214 HOH HOH . G 5 HOH A 34 634 141 HOH HOH . G 5 HOH A 35 635 23 HOH HOH . G 5 HOH A 36 636 8 HOH HOH . G 5 HOH A 37 637 54 HOH HOH . G 5 HOH A 38 638 68 HOH HOH . G 5 HOH A 39 639 102 HOH HOH . G 5 HOH A 40 640 12 HOH HOH . G 5 HOH A 41 641 14 HOH HOH . G 5 HOH A 42 642 175 HOH HOH . G 5 HOH A 43 643 40 HOH HOH . G 5 HOH A 44 644 51 HOH HOH . G 5 HOH A 45 645 145 HOH HOH . G 5 HOH A 46 646 57 HOH HOH . G 5 HOH A 47 647 6 HOH HOH . G 5 HOH A 48 648 27 HOH HOH . G 5 HOH A 49 649 115 HOH HOH . G 5 HOH A 50 650 109 HOH HOH . G 5 HOH A 51 651 24 HOH HOH . G 5 HOH A 52 652 193 HOH HOH . G 5 HOH A 53 653 49 HOH HOH . G 5 HOH A 54 654 91 HOH HOH . G 5 HOH A 55 655 44 HOH HOH . G 5 HOH A 56 656 73 HOH HOH . G 5 HOH A 57 657 53 HOH HOH . G 5 HOH A 58 658 90 HOH HOH . G 5 HOH A 59 659 111 HOH HOH . G 5 HOH A 60 660 204 HOH HOH . G 5 HOH A 61 661 132 HOH HOH . G 5 HOH A 62 662 67 HOH HOH . G 5 HOH A 63 663 92 HOH HOH . G 5 HOH A 64 664 25 HOH HOH . G 5 HOH A 65 665 26 HOH HOH . G 5 HOH A 66 666 205 HOH HOH . G 5 HOH A 67 667 70 HOH HOH . G 5 HOH A 68 668 143 HOH HOH . G 5 HOH A 69 669 32 HOH HOH . G 5 HOH A 70 670 114 HOH HOH . G 5 HOH A 71 671 22 HOH HOH . G 5 HOH A 72 672 83 HOH HOH . G 5 HOH A 73 673 209 HOH HOH . G 5 HOH A 74 674 134 HOH HOH . G 5 HOH A 75 675 196 HOH HOH . G 5 HOH A 76 676 79 HOH HOH . G 5 HOH A 77 677 168 HOH HOH . G 5 HOH A 78 678 80 HOH HOH . G 5 HOH A 79 679 29 HOH HOH . G 5 HOH A 80 680 85 HOH HOH . G 5 HOH A 81 681 100 HOH HOH . G 5 HOH A 82 682 179 HOH HOH . G 5 HOH A 83 683 9 HOH HOH . G 5 HOH A 84 684 144 HOH HOH . G 5 HOH A 85 685 116 HOH HOH . G 5 HOH A 86 686 20 HOH HOH . G 5 HOH A 87 687 150 HOH HOH . G 5 HOH A 88 688 171 HOH HOH . G 5 HOH A 89 689 5 HOH HOH . G 5 HOH A 90 690 15 HOH HOH . G 5 HOH A 91 691 65 HOH HOH . G 5 HOH A 92 692 63 HOH HOH . G 5 HOH A 93 693 77 HOH HOH . G 5 HOH A 94 694 72 HOH HOH . G 5 HOH A 95 695 7 HOH HOH . G 5 HOH A 96 696 149 HOH HOH . G 5 HOH A 97 697 10 HOH HOH . G 5 HOH A 98 698 182 HOH HOH . G 5 HOH A 99 699 30 HOH HOH . G 5 HOH A 100 700 207 HOH HOH . G 5 HOH A 101 701 48 HOH HOH . G 5 HOH A 102 702 137 HOH HOH . G 5 HOH A 103 703 76 HOH HOH . G 5 HOH A 104 704 135 HOH HOH . G 5 HOH A 105 705 203 HOH HOH . G 5 HOH A 106 706 197 HOH HOH . G 5 HOH A 107 707 11 HOH HOH . G 5 HOH A 108 708 19 HOH HOH . G 5 HOH A 109 709 190 HOH HOH . G 5 HOH A 110 710 159 HOH HOH . G 5 HOH A 111 711 45 HOH HOH . G 5 HOH A 112 712 97 HOH HOH . G 5 HOH A 113 713 71 HOH HOH . G 5 HOH A 114 714 13 HOH HOH . G 5 HOH A 115 715 42 HOH HOH . G 5 HOH A 116 716 33 HOH HOH . G 5 HOH A 117 717 37 HOH HOH . G 5 HOH A 118 718 139 HOH HOH . G 5 HOH A 119 719 41 HOH HOH . G 5 HOH A 120 720 75 HOH HOH . G 5 HOH A 121 721 18 HOH HOH . G 5 HOH A 122 722 39 HOH HOH . G 5 HOH A 123 723 200 HOH HOH . G 5 HOH A 124 724 133 HOH HOH . G 5 HOH A 125 725 160 HOH HOH . G 5 HOH A 126 726 31 HOH HOH . G 5 HOH A 127 727 216 HOH HOH . G 5 HOH A 128 728 211 HOH HOH . G 5 HOH A 129 729 21 HOH HOH . G 5 HOH A 130 730 99 HOH HOH . G 5 HOH A 131 731 121 HOH HOH . G 5 HOH A 132 732 98 HOH HOH . G 5 HOH A 133 733 47 HOH HOH . G 5 HOH A 134 734 46 HOH HOH . G 5 HOH A 135 735 17 HOH HOH . G 5 HOH A 136 736 16 HOH HOH . G 5 HOH A 137 737 81 HOH HOH . G 5 HOH A 138 738 170 HOH HOH . G 5 HOH A 139 739 136 HOH HOH . G 5 HOH A 140 740 43 HOH HOH . G 5 HOH A 141 741 105 HOH HOH . G 5 HOH A 142 742 78 HOH HOH . G 5 HOH A 143 743 101 HOH HOH . G 5 HOH A 144 744 166 HOH HOH . G 5 HOH A 145 745 142 HOH HOH . G 5 HOH A 146 746 165 HOH HOH . G 5 HOH A 147 747 169 HOH HOH . G 5 HOH A 148 748 125 HOH HOH . G 5 HOH A 149 749 212 HOH HOH . G 5 HOH A 150 750 195 HOH HOH . G 5 HOH A 151 751 206 HOH HOH . G 5 HOH A 152 752 56 HOH HOH . G 5 HOH A 153 753 103 HOH HOH . G 5 HOH A 154 754 129 HOH HOH . G 5 HOH A 155 755 208 HOH HOH . G 5 HOH A 156 756 36 HOH HOH . G 5 HOH A 157 757 184 HOH HOH . G 5 HOH A 158 758 38 HOH HOH . G 5 HOH A 159 759 118 HOH HOH . G 5 HOH A 160 760 93 HOH HOH . G 5 HOH A 161 761 120 HOH HOH . G 5 HOH A 162 762 192 HOH HOH . G 5 HOH A 163 763 104 HOH HOH . G 5 HOH A 164 764 201 HOH HOH . G 5 HOH A 165 765 59 HOH HOH . G 5 HOH A 166 766 52 HOH HOH . G 5 HOH A 167 767 61 HOH HOH . G 5 HOH A 168 768 218 HOH HOH . G 5 HOH A 169 769 94 HOH HOH . G 5 HOH A 170 770 213 HOH HOH . G 5 HOH A 171 771 180 HOH HOH . G 5 HOH A 172 772 210 HOH HOH . G 5 HOH A 173 773 202 HOH HOH . G 5 HOH A 174 774 173 HOH HOH . G 5 HOH A 175 775 161 HOH HOH . G 5 HOH A 176 776 108 HOH HOH . G 5 HOH A 177 777 126 HOH HOH . G 5 HOH A 178 778 122 HOH HOH . G 5 HOH A 179 779 198 HOH HOH . G 5 HOH A 180 780 89 HOH HOH . G 5 HOH A 181 781 199 HOH HOH . G 5 HOH A 182 782 124 HOH HOH . G 5 HOH A 183 783 154 HOH HOH . G 5 HOH A 184 784 110 HOH HOH . G 5 HOH A 185 785 86 HOH HOH . G 5 HOH A 186 786 178 HOH HOH . G 5 HOH A 187 787 140 HOH HOH . G 5 HOH A 188 788 187 HOH HOH . G 5 HOH A 189 789 117 HOH HOH . G 5 HOH A 190 790 194 HOH HOH . G 5 HOH A 191 791 215 HOH HOH . G 5 HOH A 192 792 181 HOH HOH . G 5 HOH A 193 793 219 HOH HOH . G 5 HOH A 194 794 82 HOH HOH . G 5 HOH A 195 795 189 HOH HOH . G 5 HOH A 196 796 174 HOH HOH . G 5 HOH A 197 797 186 HOH HOH . G 5 HOH A 198 798 123 HOH HOH . G 5 HOH A 199 799 221 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 20.945 6.771 17.951 1 22.44 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 20.15 6.413 19.058 1 20.9 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 19.198 5.478 18.93 1 22.29 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 18.969 4.869 17.766 1 22 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 19.74 5.19 16.659 1 20.89 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 20.737 6.161 16.77 1 21.89 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 20.313 6.947 20.169 1 24.88 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 18.063 3.999 17.695 1 24.03 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 21.985 7.798 18.093 1 23.13 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 23.386 7.207 17.988 1 22.71 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 23.775 6.65 19.235 1 23.83 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 24.214 8.403 17.565 1 22.25 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 23.222 9.217 16.729 1 24.09 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 21.898 8.753 17.043 1 21.49 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 24.66 9.138 18.713 1 19.21 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 23.408 9.029 15.239 1 21.35 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 24.579 9.742 14.851 1 21.4 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 25.47 9.292 13.604 1 22.51 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 26.61 10.265 13.527 1 23.33 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 25.809 7.828 13.803 1 27.46 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 24.581 9.319 12.264 1 27.05 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 23.534 10.423 11.711 1 27.45 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 23.551 10.068 10.249 1 23.41 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 24.128 11.756 12.06 1 28.95 ? O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 22.251 10.089 12.391 1 28.23 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #