data_5TME # _model_server_result.job_id vV4rOYxyM4Tc-4rQztIkjg _model_server_result.datetime_utc '2024-12-29 14:52:51' _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 5tme # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5TME # _exptl.entry_id 5TME _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 5TME _cell.length_a 59.067 _cell.length_b 83.306 _cell.length_c 98.249 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TME _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 _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 273 A CYS 272 1_555 A SG CYS 345 A CYS 344 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.052 ? disulf ? disulf2 A SG CYS 309 A CYS 308 1_555 A SG CYS 335 A CYS 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? # _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 5TME _atom_sites.fract_transf_matrix[1][1] 0.01693 _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] 0.012004 _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] 0.010178 _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 1 UDP UDP . C 3 HOH A 1 601 148 HOH HOH . C 3 HOH A 2 602 24 HOH HOH . C 3 HOH A 3 603 87 HOH HOH . C 3 HOH A 4 604 197 HOH HOH . C 3 HOH A 5 605 168 HOH HOH . C 3 HOH A 6 606 140 HOH HOH . C 3 HOH A 7 607 35 HOH HOH . C 3 HOH A 8 608 137 HOH HOH . C 3 HOH A 9 609 104 HOH HOH . C 3 HOH A 10 610 16 HOH HOH . C 3 HOH A 11 611 163 HOH HOH . C 3 HOH A 12 612 1 HOH HOH . C 3 HOH A 13 613 166 HOH HOH . C 3 HOH A 14 614 190 HOH HOH . C 3 HOH A 15 615 93 HOH HOH . C 3 HOH A 16 616 67 HOH HOH . C 3 HOH A 17 617 144 HOH HOH . C 3 HOH A 18 618 91 HOH HOH . C 3 HOH A 19 619 21 HOH HOH . C 3 HOH A 20 620 194 HOH HOH . C 3 HOH A 21 621 159 HOH HOH . C 3 HOH A 22 622 82 HOH HOH . C 3 HOH A 23 623 55 HOH HOH . C 3 HOH A 24 624 34 HOH HOH . C 3 HOH A 25 625 71 HOH HOH . C 3 HOH A 26 626 100 HOH HOH . C 3 HOH A 27 627 173 HOH HOH . C 3 HOH A 28 628 69 HOH HOH . C 3 HOH A 29 629 124 HOH HOH . C 3 HOH A 30 630 66 HOH HOH . C 3 HOH A 31 631 83 HOH HOH . C 3 HOH A 32 632 107 HOH HOH . C 3 HOH A 33 633 50 HOH HOH . C 3 HOH A 34 634 13 HOH HOH . C 3 HOH A 35 635 145 HOH HOH . C 3 HOH A 36 636 126 HOH HOH . C 3 HOH A 37 637 19 HOH HOH . C 3 HOH A 38 638 185 HOH HOH . C 3 HOH A 39 639 139 HOH HOH . C 3 HOH A 40 640 49 HOH HOH . C 3 HOH A 41 641 7 HOH HOH . C 3 HOH A 42 642 25 HOH HOH . C 3 HOH A 43 643 123 HOH HOH . C 3 HOH A 44 644 132 HOH HOH . C 3 HOH A 45 645 193 HOH HOH . C 3 HOH A 46 646 32 HOH HOH . C 3 HOH A 47 647 74 HOH HOH . C 3 HOH A 48 648 94 HOH HOH . C 3 HOH A 49 649 154 HOH HOH . C 3 HOH A 50 650 136 HOH HOH . C 3 HOH A 51 651 20 HOH HOH . C 3 HOH A 52 652 45 HOH HOH . C 3 HOH A 53 653 58 HOH HOH . C 3 HOH A 54 654 14 HOH HOH . C 3 HOH A 55 655 62 HOH HOH . C 3 HOH A 56 656 153 HOH HOH . C 3 HOH A 57 657 47 HOH HOH . C 3 HOH A 58 658 146 HOH HOH . C 3 HOH A 59 659 12 HOH HOH . C 3 HOH A 60 660 81 HOH HOH . C 3 HOH A 61 661 30 HOH HOH . C 3 HOH A 62 662 8 HOH HOH . C 3 HOH A 63 663 127 HOH HOH . C 3 HOH A 64 664 141 HOH HOH . C 3 HOH A 65 665 165 HOH HOH . C 3 HOH A 66 666 152 HOH HOH . C 3 HOH A 67 667 5 HOH HOH . C 3 HOH A 68 668 189 HOH HOH . C 3 HOH A 69 669 175 HOH HOH . C 3 HOH A 70 670 75 HOH HOH . C 3 HOH A 71 671 38 HOH HOH . C 3 HOH A 72 672 86 HOH HOH . C 3 HOH A 73 673 53 HOH HOH . C 3 HOH A 74 674 95 HOH HOH . C 3 HOH A 75 675 44 HOH HOH . C 3 HOH A 76 676 88 HOH HOH . C 3 HOH A 77 677 41 HOH HOH . C 3 HOH A 78 678 113 HOH HOH . C 3 HOH A 79 679 133 HOH HOH . C 3 HOH A 80 680 72 HOH HOH . C 3 HOH A 81 681 84 HOH HOH . C 3 HOH A 82 682 37 HOH HOH . C 3 HOH A 83 683 73 HOH HOH . C 3 HOH A 84 684 15 HOH HOH . C 3 HOH A 85 685 106 HOH HOH . C 3 HOH A 86 686 51 HOH HOH . C 3 HOH A 87 687 125 HOH HOH . C 3 HOH A 88 688 68 HOH HOH . C 3 HOH A 89 689 63 HOH HOH . C 3 HOH A 90 690 184 HOH HOH . C 3 HOH A 91 691 102 HOH HOH . C 3 HOH A 92 692 103 HOH HOH . C 3 HOH A 93 693 4 HOH HOH . C 3 HOH A 94 694 23 HOH HOH . C 3 HOH A 95 695 131 HOH HOH . C 3 HOH A 96 696 22 HOH HOH . C 3 HOH A 97 697 26 HOH HOH . C 3 HOH A 98 698 18 HOH HOH . C 3 HOH A 99 699 89 HOH HOH . C 3 HOH A 100 700 80 HOH HOH . C 3 HOH A 101 701 39 HOH HOH . C 3 HOH A 102 702 195 HOH HOH . C 3 HOH A 103 703 61 HOH HOH . C 3 HOH A 104 704 156 HOH HOH . C 3 HOH A 105 705 52 HOH HOH . C 3 HOH A 106 706 33 HOH HOH . C 3 HOH A 107 707 46 HOH HOH . C 3 HOH A 108 708 28 HOH HOH . C 3 HOH A 109 709 54 HOH HOH . C 3 HOH A 110 710 162 HOH HOH . C 3 HOH A 111 711 3 HOH HOH . C 3 HOH A 112 712 17 HOH HOH . C 3 HOH A 113 713 128 HOH HOH . C 3 HOH A 114 714 78 HOH HOH . C 3 HOH A 115 715 11 HOH HOH . C 3 HOH A 116 716 9 HOH HOH . C 3 HOH A 117 717 130 HOH HOH . C 3 HOH A 118 718 85 HOH HOH . C 3 HOH A 119 719 199 HOH HOH . C 3 HOH A 120 720 122 HOH HOH . C 3 HOH A 121 721 40 HOH HOH . C 3 HOH A 122 722 111 HOH HOH . C 3 HOH A 123 723 96 HOH HOH . C 3 HOH A 124 724 99 HOH HOH . C 3 HOH A 125 725 90 HOH HOH . C 3 HOH A 126 726 98 HOH HOH . C 3 HOH A 127 727 92 HOH HOH . C 3 HOH A 128 728 108 HOH HOH . C 3 HOH A 129 729 192 HOH HOH . C 3 HOH A 130 730 29 HOH HOH . C 3 HOH A 131 731 135 HOH HOH . C 3 HOH A 132 732 191 HOH HOH . C 3 HOH A 133 733 42 HOH HOH . C 3 HOH A 134 734 180 HOH HOH . C 3 HOH A 135 735 160 HOH HOH . C 3 HOH A 136 736 178 HOH HOH . C 3 HOH A 137 737 43 HOH HOH . C 3 HOH A 138 738 174 HOH HOH . C 3 HOH A 139 739 2 HOH HOH . C 3 HOH A 140 740 169 HOH HOH . C 3 HOH A 141 741 129 HOH HOH . C 3 HOH A 142 742 27 HOH HOH . C 3 HOH A 143 743 171 HOH HOH . C 3 HOH A 144 744 6 HOH HOH . C 3 HOH A 145 745 155 HOH HOH . C 3 HOH A 146 746 10 HOH HOH . C 3 HOH A 147 747 172 HOH HOH . C 3 HOH A 148 748 182 HOH HOH . C 3 HOH A 149 749 158 HOH HOH . C 3 HOH A 150 750 134 HOH HOH . C 3 HOH A 151 751 109 HOH HOH . C 3 HOH A 152 752 181 HOH HOH . C 3 HOH A 153 753 59 HOH HOH . C 3 HOH A 154 754 196 HOH HOH . C 3 HOH A 155 755 142 HOH HOH . C 3 HOH A 156 756 164 HOH HOH . C 3 HOH A 157 757 167 HOH HOH . C 3 HOH A 158 758 97 HOH HOH . C 3 HOH A 159 759 176 HOH HOH . C 3 HOH A 160 760 36 HOH HOH . C 3 HOH A 161 761 70 HOH HOH . C 3 HOH A 162 762 31 HOH HOH . C 3 HOH A 163 763 48 HOH HOH . C 3 HOH A 164 764 170 HOH HOH . C 3 HOH A 165 765 105 HOH HOH . C 3 HOH A 166 766 179 HOH HOH . C 3 HOH A 167 767 157 HOH HOH . C 3 HOH A 168 768 186 HOH HOH . C 3 HOH A 169 769 183 HOH HOH . C 3 HOH A 170 770 143 HOH HOH . C 3 HOH A 171 771 138 HOH HOH . C 3 HOH A 172 772 57 HOH HOH . C 3 HOH A 173 773 187 HOH HOH . C 3 HOH A 174 774 188 HOH HOH . C 3 HOH A 175 775 149 HOH HOH . C 3 HOH A 176 776 118 HOH HOH . C 3 HOH A 177 777 198 HOH HOH . C 3 HOH A 178 778 64 HOH HOH . C 3 HOH A 179 779 117 HOH HOH . C 3 HOH A 180 780 101 HOH HOH . C 3 HOH A 181 781 177 HOH HOH . C 3 HOH A 182 782 79 HOH HOH . C 3 HOH A 183 783 76 HOH HOH . C 3 HOH A 184 784 147 HOH HOH . C 3 HOH A 185 785 161 HOH HOH . C 3 HOH A 186 786 151 HOH HOH . C 3 HOH A 187 787 120 HOH HOH . C 3 HOH A 188 788 119 HOH HOH . C 3 HOH A 189 789 110 HOH HOH . C 3 HOH A 190 790 77 HOH HOH . C 3 HOH A 191 791 56 HOH HOH . C 3 HOH A 192 792 115 HOH HOH . C 3 HOH A 193 793 114 HOH HOH . C 3 HOH A 194 794 150 HOH HOH . C 3 HOH A 195 795 116 HOH HOH . C 3 HOH A 196 796 112 HOH HOH . C 3 HOH A 197 797 60 HOH HOH . C 3 HOH A 198 798 65 HOH HOH . C 3 HOH A 199 799 121 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 8.197 3.018 -1.739 1 29.42 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 7.861 3.309 -0.378 1 26.38 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 6.552 3.326 -0.051 1 26.96 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 5.585 3.011 -0.926 1 28.41 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 5.891 2.71 -2.249 1 31.1 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 7.213 2.705 -2.615 1 27.9 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 8.719 3.553 0.521 1 28.98 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 4.381 3.091 -0.561 1 27.47 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 9.574 3.001 -2.286 1 30.9 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 10.158 1.596 -2.268 1 25.4 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 10.709 1.303 -0.988 1 25.02 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 11.184 1.651 -3.4 1 24.16 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 10.407 2.417 -4.562 1 32.53 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 9.655 3.417 -3.7 1 35.74 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 12.332 2.298 -2.866 1 27.25 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 9.651 1.447 -5.567 1 31.19 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 10.587 0.879 -6.669 1 34.76 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 10.797 -0.459 -7.553 1 30.45 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 12.221 -0.481 -8.241 1 29 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 10.628 -1.739 -6.848 1 27.02 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 9.63 -0.257 -8.776 1 31.68 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 8.959 1.174 -9.377 1 38.39 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 8.156 0.476 -10.451 1 32.05 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 8.216 1.885 -8.212 1 36 ? O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 10.173 1.927 -9.967 1 40.67 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 83 _model_server_stats.parse_time_ms 40 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 388 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #