data_8INJ # _model_server_result.job_id FS0V4JQQWFl1VtxM3XEWbw _model_server_result.datetime_utc '2025-02-18 07:30:57' _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 8inj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8INJ # _exptl.entry_id 8INJ _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 8INJ _cell.length_a 45.718 _cell.length_b 52.21 _cell.length_c 201.48 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8INJ _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 442 n n N1 C6 UDP sing 443 n n N1 C1' UDP sing 444 n n C2 N3 UDP sing 445 n n C2 O2 UDP doub 446 n n N3 C4 UDP sing 447 n n N3 HN3 UDP sing 448 n n C4 C5 UDP sing 449 n n C4 O4 UDP doub 450 n n C5 C6 UDP doub 451 n n C5 H5 UDP sing 452 n n C6 H6 UDP sing 453 n n C1' C2' UDP sing 454 n n C1' O4' UDP sing 455 n n C1' H1' UDP sing 456 n n C2' O2' UDP sing 457 n n C2' C3' UDP sing 458 n n C2' H2' UDP sing 459 n n O2' HO2' UDP sing 460 n n C3' C4' UDP sing 461 n n C3' O3' UDP sing 462 n n C3' H3' UDP sing 463 n n C4' O4' UDP sing 464 n n C4' C5' UDP sing 465 n n C4' H4' UDP sing 466 n n O3' HO3' UDP sing 467 n n C5' O5' UDP sing 468 n n C5' "H5'1" UDP sing 469 n n C5' "H5'2" UDP sing 470 n n O5' PA UDP sing 471 n n PA O1A UDP doub 472 n n PA O2A UDP sing 473 n n PA O3A UDP sing 474 n n O2A HOA2 UDP sing 475 n n O3A PB UDP sing 476 n n PB O1B UDP doub 477 n n PB O2B UDP sing 478 n n PB O3B UDP sing 479 n n O2B HOB2 UDP sing 480 n n O3B HOB3 UDP sing 481 n n # _atom_sites.entry_id 8INJ _atom_sites.fract_transf_matrix[1][1] 0.021873 _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] 0.019153 _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] 0.004963 _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 DTX A 1 502 503 DTX DRG . D 4 TRS A 1 503 504 TRS TRS . E 5 HOH A 1 601 164 HOH HOH . E 5 HOH A 2 602 206 HOH HOH . E 5 HOH A 3 603 38 HOH HOH . E 5 HOH A 4 604 142 HOH HOH . E 5 HOH A 5 605 208 HOH HOH . E 5 HOH A 6 606 93 HOH HOH . E 5 HOH A 7 607 59 HOH HOH . E 5 HOH A 8 608 77 HOH HOH . E 5 HOH A 9 609 178 HOH HOH . E 5 HOH A 10 610 242 HOH HOH . E 5 HOH A 11 611 29 HOH HOH . E 5 HOH A 12 612 10 HOH HOH . E 5 HOH A 13 613 41 HOH HOH . E 5 HOH A 14 614 20 HOH HOH . E 5 HOH A 15 615 100 HOH HOH . E 5 HOH A 16 616 21 HOH HOH . E 5 HOH A 17 617 192 HOH HOH . E 5 HOH A 18 618 39 HOH HOH . E 5 HOH A 19 619 232 HOH HOH . E 5 HOH A 20 620 6 HOH HOH . E 5 HOH A 21 621 149 HOH HOH . E 5 HOH A 22 622 18 HOH HOH . E 5 HOH A 23 623 5 HOH HOH . E 5 HOH A 24 624 137 HOH HOH . E 5 HOH A 25 625 1 HOH HOH . E 5 HOH A 26 626 8 HOH HOH . E 5 HOH A 27 627 30 HOH HOH . E 5 HOH A 28 628 2 HOH HOH . E 5 HOH A 29 629 3 HOH HOH . E 5 HOH A 30 630 94 HOH HOH . E 5 HOH A 31 631 79 HOH HOH . E 5 HOH A 32 632 205 HOH HOH . E 5 HOH A 33 633 4 HOH HOH . E 5 HOH A 34 634 51 HOH HOH . E 5 HOH A 35 635 121 HOH HOH . E 5 HOH A 36 636 233 HOH HOH . E 5 HOH A 37 637 154 HOH HOH . E 5 HOH A 38 638 23 HOH HOH . E 5 HOH A 39 639 146 HOH HOH . E 5 HOH A 40 640 57 HOH HOH . E 5 HOH A 41 641 106 HOH HOH . E 5 HOH A 42 642 7 HOH HOH . E 5 HOH A 43 643 33 HOH HOH . E 5 HOH A 44 644 46 HOH HOH . E 5 HOH A 45 645 48 HOH HOH . E 5 HOH A 46 646 19 HOH HOH . E 5 HOH A 47 647 85 HOH HOH . E 5 HOH A 48 648 31 HOH HOH . E 5 HOH A 49 649 16 HOH HOH . E 5 HOH A 50 650 32 HOH HOH . E 5 HOH A 51 651 172 HOH HOH . E 5 HOH A 52 652 42 HOH HOH . E 5 HOH A 53 653 107 HOH HOH . E 5 HOH A 54 654 246 HOH HOH . E 5 HOH A 55 655 43 HOH HOH . E 5 HOH A 56 656 220 HOH HOH . E 5 HOH A 57 657 97 HOH HOH . E 5 HOH A 58 658 165 HOH HOH . E 5 HOH A 59 659 99 HOH HOH . E 5 HOH A 60 660 49 HOH HOH . E 5 HOH A 61 661 81 HOH HOH . E 5 HOH A 62 662 102 HOH HOH . E 5 HOH A 63 663 54 HOH HOH . E 5 HOH A 64 664 80 HOH HOH . E 5 HOH A 65 665 56 HOH HOH . E 5 HOH A 66 666 118 HOH HOH . E 5 HOH A 67 667 17 HOH HOH . E 5 HOH A 68 668 114 HOH HOH . E 5 HOH A 69 669 67 HOH HOH . E 5 HOH A 70 670 28 HOH HOH . E 5 HOH A 71 671 9 HOH HOH . E 5 HOH A 72 672 65 HOH HOH . E 5 HOH A 73 673 159 HOH HOH . E 5 HOH A 74 674 58 HOH HOH . E 5 HOH A 75 675 130 HOH HOH . E 5 HOH A 76 676 139 HOH HOH . E 5 HOH A 77 677 184 HOH HOH . E 5 HOH A 78 678 72 HOH HOH . E 5 HOH A 79 679 15 HOH HOH . E 5 HOH A 80 680 36 HOH HOH . E 5 HOH A 81 681 14 HOH HOH . E 5 HOH A 82 682 176 HOH HOH . E 5 HOH A 83 683 201 HOH HOH . E 5 HOH A 84 684 122 HOH HOH . E 5 HOH A 85 685 214 HOH HOH . E 5 HOH A 86 686 62 HOH HOH . E 5 HOH A 87 687 230 HOH HOH . E 5 HOH A 88 688 35 HOH HOH . E 5 HOH A 89 689 91 HOH HOH . E 5 HOH A 90 690 131 HOH HOH . E 5 HOH A 91 691 148 HOH HOH . E 5 HOH A 92 692 27 HOH HOH . E 5 HOH A 93 693 183 HOH HOH . E 5 HOH A 94 694 175 HOH HOH . E 5 HOH A 95 695 112 HOH HOH . E 5 HOH A 96 696 98 HOH HOH . E 5 HOH A 97 697 90 HOH HOH . E 5 HOH A 98 698 73 HOH HOH . E 5 HOH A 99 699 239 HOH HOH . E 5 HOH A 100 700 61 HOH HOH . E 5 HOH A 101 701 179 HOH HOH . E 5 HOH A 102 702 157 HOH HOH . E 5 HOH A 103 703 84 HOH HOH . E 5 HOH A 104 704 11 HOH HOH . E 5 HOH A 105 705 26 HOH HOH . E 5 HOH A 106 706 89 HOH HOH . E 5 HOH A 107 707 167 HOH HOH . E 5 HOH A 108 708 116 HOH HOH . E 5 HOH A 109 709 74 HOH HOH . E 5 HOH A 110 710 95 HOH HOH . E 5 HOH A 111 711 34 HOH HOH . E 5 HOH A 112 712 12 HOH HOH . E 5 HOH A 113 713 69 HOH HOH . E 5 HOH A 114 714 195 HOH HOH . E 5 HOH A 115 715 152 HOH HOH . E 5 HOH A 116 716 134 HOH HOH . E 5 HOH A 117 717 231 HOH HOH . E 5 HOH A 118 718 50 HOH HOH . E 5 HOH A 119 719 105 HOH HOH . E 5 HOH A 120 720 87 HOH HOH . E 5 HOH A 121 721 76 HOH HOH . E 5 HOH A 122 722 126 HOH HOH . E 5 HOH A 123 723 103 HOH HOH . E 5 HOH A 124 724 75 HOH HOH . E 5 HOH A 125 725 78 HOH HOH . E 5 HOH A 126 726 60 HOH HOH . E 5 HOH A 127 727 171 HOH HOH . E 5 HOH A 128 728 194 HOH HOH . E 5 HOH A 129 729 197 HOH HOH . E 5 HOH A 130 730 243 HOH HOH . E 5 HOH A 131 731 92 HOH HOH . E 5 HOH A 132 732 110 HOH HOH . E 5 HOH A 133 733 104 HOH HOH . E 5 HOH A 134 734 64 HOH HOH . E 5 HOH A 135 735 13 HOH HOH . E 5 HOH A 136 736 52 HOH HOH . E 5 HOH A 137 737 143 HOH HOH . E 5 HOH A 138 738 207 HOH HOH . E 5 HOH A 139 739 140 HOH HOH . E 5 HOH A 140 740 202 HOH HOH . E 5 HOH A 141 741 45 HOH HOH . E 5 HOH A 142 742 216 HOH HOH . E 5 HOH A 143 743 153 HOH HOH . E 5 HOH A 144 744 113 HOH HOH . E 5 HOH A 145 745 150 HOH HOH . E 5 HOH A 146 746 225 HOH HOH . E 5 HOH A 147 747 161 HOH HOH . E 5 HOH A 148 748 173 HOH HOH . E 5 HOH A 149 749 55 HOH HOH . E 5 HOH A 150 750 227 HOH HOH . E 5 HOH A 151 751 209 HOH HOH . E 5 HOH A 152 752 187 HOH HOH . E 5 HOH A 153 753 22 HOH HOH . E 5 HOH A 154 754 119 HOH HOH . E 5 HOH A 155 755 141 HOH HOH . E 5 HOH A 156 756 86 HOH HOH . E 5 HOH A 157 757 123 HOH HOH . E 5 HOH A 158 758 177 HOH HOH . E 5 HOH A 159 759 191 HOH HOH . E 5 HOH A 160 760 224 HOH HOH . E 5 HOH A 161 761 235 HOH HOH . E 5 HOH A 162 762 245 HOH HOH . E 5 HOH A 163 763 221 HOH HOH . E 5 HOH A 164 764 37 HOH HOH . E 5 HOH A 165 765 108 HOH HOH . E 5 HOH A 166 766 158 HOH HOH . E 5 HOH A 167 767 210 HOH HOH . E 5 HOH A 168 768 190 HOH HOH . E 5 HOH A 169 769 203 HOH HOH . E 5 HOH A 170 770 211 HOH HOH . E 5 HOH A 171 771 181 HOH HOH . E 5 HOH A 172 772 82 HOH HOH . E 5 HOH A 173 773 170 HOH HOH . E 5 HOH A 174 774 212 HOH HOH . E 5 HOH A 175 775 168 HOH HOH . E 5 HOH A 176 776 241 HOH HOH . E 5 HOH A 177 777 196 HOH HOH . E 5 HOH A 178 778 244 HOH HOH . E 5 HOH A 179 779 151 HOH HOH . E 5 HOH A 180 780 236 HOH HOH . E 5 HOH A 181 781 217 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 -4.483 20.791 80.751 1 27.76 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 -3.398 20.244 81.283 1 27.45 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 -2.717 20.831 82.237 1 26.69 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 -3.112 22.004 82.698 1 27.82 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 -4.242 22.641 82.185 1 27.24 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 -4.917 21.977 81.16 1 26.64 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 -2.97 18.992 80.843 1 25.81 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 -2.371 22.585 83.692 1 31.08 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 -5.174 20.118 79.633 1 28.17 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 -6.585 19.597 79.907 1 25.12 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 -6.475 18.326 80.391 1 26.94 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 -7.157 19.607 78.467 1 26.5 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 -6.698 20.716 77.924 1 22.95 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 -5.327 21.023 78.673 1 26.69 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 -6.611 18.428 77.729 1 26.39 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 -7.647 21.878 78.193 1 27.7 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 -8.659 21.773 77.225 1 24.04 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 -10.113 22.501 77.425 1 25.8 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 -11.114 21.907 76.473 1 24.47 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 -10.546 22.288 78.878 1 25.84 -1 O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 -9.949 24.121 77.277 1 26.22 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 -9.098 24.958 76.15 1 25.84 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 -9.258 24.273 74.798 1 25.43 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 -9.718 26.321 76.179 1 27.23 -1 O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 -7.636 24.98 76.54 1 25.4 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #