data_1BQ1 # _model_server_result.job_id J4tcRgzH_hRbri-xWs-ntg _model_server_result.datetime_utc '2025-02-17 10:31:38' _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 1bq1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":567}' # _entry.id 1BQ1 # _exptl.entry_id 1BQ1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 1BQ1 _cell.length_a 127.221 _cell.length_b 127.221 _cell.length_c 68.178 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BQ1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 covale ? covale1 A C CXM 1 A CXM 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A SG CYS 146 A CYS 146 1_555 C C6 UMP . A UMP 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? covale ? covale3 B C CXM 1 B CXM 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale4 B SG CYS 146 B CYS 146 1_555 E C6 UMP . B UMP 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.837 ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 440 n n N1 C6 UMP sing 441 n n N1 C1' UMP sing 442 n n C2 N3 UMP sing 443 n n C2 O2 UMP doub 444 n n N3 C4 UMP sing 445 n n N3 HN3 UMP sing 446 n n C4 C5 UMP sing 447 n n C4 O4 UMP doub 448 n n C5 C6 UMP doub 449 n n C5 H5 UMP sing 450 n n C6 H6 UMP sing 451 n n C1' C2' UMP sing 452 n n C1' O4' UMP sing 453 n n C1' H1' UMP sing 454 n n C2' C3' UMP sing 455 n n C2' H2' UMP sing 456 n n C2' "H2''" UMP sing 457 n n C3' C4' UMP sing 458 n n C3' O3' UMP sing 459 n n C3' H3' UMP sing 460 n n C4' O4' UMP sing 461 n n C4' C5' UMP sing 462 n n C4' H4' UMP sing 463 n n O3' HO3' UMP sing 464 n n C5' O5' UMP sing 465 n n C5' H5' UMP sing 466 n n C5' "H5''" UMP sing 467 n n O5' P UMP sing 468 n n P OP1 UMP doub 469 n n P OP2 UMP sing 470 n n P OP3 UMP sing 471 n n OP2 HOP2 UMP sing 472 n n OP3 HOP3 UMP sing 473 n n # _atom_sites.entry_id 1BQ1 _atom_sites.fract_transf_matrix[1][1] 0.00786 _atom_sites.fract_transf_matrix[1][2] 0.004538 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009076 _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] 0.014667 _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 C 2 UMP A 1 565 565 UMP UMP . D 3 CB3 A 1 566 566 CB3 CB3 . E 2 UMP B 1 567 567 UMP UMP . F 3 CB3 B 1 568 568 CB3 CB3 . G 4 HOH A 1 602 602 HOH HOH . G 4 HOH A 2 603 603 HOH HOH . G 4 HOH A 3 604 604 HOH HOH . G 4 HOH A 4 605 605 HOH HOH . G 4 HOH A 5 606 606 HOH HOH . G 4 HOH A 6 608 608 HOH HOH . G 4 HOH A 7 609 609 HOH HOH . G 4 HOH A 8 610 610 HOH HOH . G 4 HOH A 9 611 611 HOH HOH . G 4 HOH A 10 612 612 HOH HOH . G 4 HOH A 11 613 613 HOH HOH . G 4 HOH A 12 614 614 HOH HOH . G 4 HOH A 13 615 615 HOH HOH . G 4 HOH A 14 616 616 HOH HOH . G 4 HOH A 15 617 617 HOH HOH . G 4 HOH A 16 618 618 HOH HOH . G 4 HOH A 17 620 620 HOH HOH . G 4 HOH A 18 623 623 HOH HOH . G 4 HOH A 19 625 625 HOH HOH . G 4 HOH A 20 627 627 HOH HOH . G 4 HOH A 21 628 628 HOH HOH . G 4 HOH A 22 629 629 HOH HOH . G 4 HOH A 23 630 630 HOH HOH . G 4 HOH A 24 631 631 HOH HOH . G 4 HOH A 25 633 633 HOH HOH . G 4 HOH A 26 634 634 HOH HOH . G 4 HOH A 27 635 635 HOH HOH . G 4 HOH A 28 636 636 HOH HOH . G 4 HOH A 29 637 637 HOH HOH . G 4 HOH A 30 639 639 HOH HOH . G 4 HOH A 31 640 640 HOH HOH . G 4 HOH A 32 641 641 HOH HOH . G 4 HOH A 33 649 649 HOH HOH . G 4 HOH A 34 650 650 HOH HOH . G 4 HOH A 35 652 652 HOH HOH . G 4 HOH A 36 653 653 HOH HOH . G 4 HOH A 37 654 654 HOH HOH . G 4 HOH A 38 656 656 HOH HOH . G 4 HOH A 39 657 657 HOH HOH . G 4 HOH A 40 658 658 HOH HOH . G 4 HOH A 41 660 660 HOH HOH . G 4 HOH A 42 661 661 HOH HOH . G 4 HOH A 43 662 662 HOH HOH . G 4 HOH A 44 663 663 HOH HOH . G 4 HOH A 45 664 664 HOH HOH . G 4 HOH A 46 665 665 HOH HOH . G 4 HOH A 47 666 666 HOH HOH . G 4 HOH A 48 667 667 HOH HOH . G 4 HOH A 49 668 668 HOH HOH . G 4 HOH A 50 669 669 HOH HOH . G 4 HOH A 51 670 670 HOH HOH . G 4 HOH A 52 671 671 HOH HOH . G 4 HOH A 53 674 674 HOH HOH . G 4 HOH A 54 677 677 HOH HOH . G 4 HOH A 55 679 679 HOH HOH . G 4 HOH A 56 680 680 HOH HOH . G 4 HOH A 57 681 681 HOH HOH . G 4 HOH A 58 682 682 HOH HOH . G 4 HOH A 59 683 683 HOH HOH . G 4 HOH A 60 685 685 HOH HOH . G 4 HOH A 61 686 686 HOH HOH . G 4 HOH A 62 687 687 HOH HOH . G 4 HOH A 63 688 688 HOH HOH . G 4 HOH A 64 689 689 HOH HOH . G 4 HOH A 65 690 690 HOH HOH . G 4 HOH A 66 691 691 HOH HOH . G 4 HOH A 67 694 694 HOH HOH . G 4 HOH A 68 695 695 HOH HOH . G 4 HOH A 69 696 696 HOH HOH . G 4 HOH A 70 697 697 HOH HOH . G 4 HOH A 71 698 698 HOH HOH . G 4 HOH A 72 699 699 HOH HOH . G 4 HOH A 73 700 700 HOH HOH . G 4 HOH A 74 701 701 HOH HOH . G 4 HOH A 75 702 702 HOH HOH . G 4 HOH A 76 703 703 HOH HOH . G 4 HOH A 77 705 705 HOH HOH . G 4 HOH A 78 707 707 HOH HOH . G 4 HOH A 79 708 708 HOH HOH . G 4 HOH A 80 709 709 HOH HOH . G 4 HOH A 81 711 711 HOH HOH . G 4 HOH A 82 712 712 HOH HOH . G 4 HOH A 83 713 713 HOH HOH . G 4 HOH A 84 714 714 HOH HOH . G 4 HOH A 85 715 715 HOH HOH . G 4 HOH A 86 716 716 HOH HOH . G 4 HOH A 87 717 717 HOH HOH . G 4 HOH A 88 718 718 HOH HOH . G 4 HOH A 89 720 720 HOH HOH . G 4 HOH A 90 721 721 HOH HOH . G 4 HOH A 91 723 723 HOH HOH . G 4 HOH A 92 726 726 HOH HOH . G 4 HOH A 93 727 727 HOH HOH . G 4 HOH A 94 728 728 HOH HOH . G 4 HOH A 95 734 734 HOH HOH . G 4 HOH A 96 741 741 HOH HOH . G 4 HOH A 97 748 748 HOH HOH . G 4 HOH A 98 749 749 HOH HOH . G 4 HOH A 99 751 751 HOH HOH . G 4 HOH A 100 752 752 HOH HOH . G 4 HOH A 101 753 753 HOH HOH . G 4 HOH A 102 755 755 HOH HOH . G 4 HOH A 103 764 764 HOH HOH . G 4 HOH A 104 768 768 HOH HOH . G 4 HOH A 105 770 770 HOH HOH . G 4 HOH A 106 773 773 HOH HOH . G 4 HOH A 107 774 774 HOH HOH . G 4 HOH A 108 775 775 HOH HOH . G 4 HOH A 109 776 776 HOH HOH . G 4 HOH A 110 777 777 HOH HOH . G 4 HOH A 111 778 778 HOH HOH . G 4 HOH A 112 779 779 HOH HOH . G 4 HOH A 113 780 780 HOH HOH . G 4 HOH A 114 781 781 HOH HOH . G 4 HOH A 115 782 782 HOH HOH . G 4 HOH A 116 790 790 HOH HOH . G 4 HOH A 117 798 798 HOH HOH . G 4 HOH A 118 824 824 HOH HOH . G 4 HOH A 119 832 832 HOH HOH . G 4 HOH A 120 833 833 HOH HOH . G 4 HOH A 121 834 834 HOH HOH . G 4 HOH A 122 835 835 HOH HOH . G 4 HOH A 123 836 836 HOH HOH . G 4 HOH A 124 838 838 HOH HOH . G 4 HOH A 125 839 839 HOH HOH . G 4 HOH A 126 840 840 HOH HOH . G 4 HOH A 127 842 842 HOH HOH . G 4 HOH A 128 843 843 HOH HOH . G 4 HOH A 129 844 844 HOH HOH . G 4 HOH A 130 845 845 HOH HOH . G 4 HOH A 131 846 846 HOH HOH . G 4 HOH A 132 849 849 HOH HOH . G 4 HOH A 133 850 850 HOH HOH . G 4 HOH A 134 851 851 HOH HOH . G 4 HOH A 135 852 852 HOH HOH . G 4 HOH A 136 901 901 HOH HOH . G 4 HOH A 137 903 903 HOH HOH . G 4 HOH A 138 904 904 HOH HOH . G 4 HOH A 139 910 910 HOH HOH . G 4 HOH A 140 911 911 HOH HOH . H 4 HOH B 1 607 607 HOH HOH . H 4 HOH B 2 619 619 HOH HOH . H 4 HOH B 3 621 621 HOH HOH . H 4 HOH B 4 622 622 HOH HOH . H 4 HOH B 5 624 624 HOH HOH . H 4 HOH B 6 632 632 HOH HOH . H 4 HOH B 7 638 638 HOH HOH . H 4 HOH B 8 642 642 HOH HOH . H 4 HOH B 9 643 643 HOH HOH . H 4 HOH B 10 644 644 HOH HOH . H 4 HOH B 11 645 645 HOH HOH . H 4 HOH B 12 646 646 HOH HOH . H 4 HOH B 13 647 647 HOH HOH . H 4 HOH B 14 648 648 HOH HOH . H 4 HOH B 15 651 651 HOH HOH . H 4 HOH B 16 672 672 HOH HOH . H 4 HOH B 17 684 684 HOH HOH . H 4 HOH B 18 704 704 HOH HOH . H 4 HOH B 19 729 729 HOH HOH . H 4 HOH B 20 730 730 HOH HOH . H 4 HOH B 21 737 737 HOH HOH . H 4 HOH B 22 739 739 HOH HOH . H 4 HOH B 23 740 740 HOH HOH . H 4 HOH B 24 742 742 HOH HOH . H 4 HOH B 25 744 744 HOH HOH . H 4 HOH B 26 745 745 HOH HOH . H 4 HOH B 27 746 746 HOH HOH . H 4 HOH B 28 747 747 HOH HOH . H 4 HOH B 29 750 750 HOH HOH . H 4 HOH B 30 754 754 HOH HOH . H 4 HOH B 31 756 756 HOH HOH . H 4 HOH B 32 758 758 HOH HOH . H 4 HOH B 33 759 759 HOH HOH . H 4 HOH B 34 760 760 HOH HOH . H 4 HOH B 35 761 761 HOH HOH . H 4 HOH B 36 762 762 HOH HOH . H 4 HOH B 37 763 763 HOH HOH . H 4 HOH B 38 765 765 HOH HOH . H 4 HOH B 39 766 766 HOH HOH . H 4 HOH B 40 767 767 HOH HOH . H 4 HOH B 41 769 769 HOH HOH . H 4 HOH B 42 771 771 HOH HOH . H 4 HOH B 43 772 772 HOH HOH . H 4 HOH B 44 783 783 HOH HOH . H 4 HOH B 45 784 784 HOH HOH . H 4 HOH B 46 785 785 HOH HOH . H 4 HOH B 47 786 786 HOH HOH . H 4 HOH B 48 787 787 HOH HOH . H 4 HOH B 49 788 788 HOH HOH . H 4 HOH B 50 791 791 HOH HOH . H 4 HOH B 51 792 792 HOH HOH . H 4 HOH B 52 793 793 HOH HOH . H 4 HOH B 53 794 794 HOH HOH . H 4 HOH B 54 795 795 HOH HOH . H 4 HOH B 55 796 796 HOH HOH . H 4 HOH B 56 797 797 HOH HOH . H 4 HOH B 57 801 801 HOH HOH . H 4 HOH B 58 802 802 HOH HOH . H 4 HOH B 59 803 803 HOH HOH . H 4 HOH B 60 804 804 HOH HOH . H 4 HOH B 61 806 806 HOH HOH . H 4 HOH B 62 807 807 HOH HOH . H 4 HOH B 63 809 809 HOH HOH . H 4 HOH B 64 810 810 HOH HOH . H 4 HOH B 65 811 811 HOH HOH . H 4 HOH B 66 812 812 HOH HOH . H 4 HOH B 67 813 813 HOH HOH . H 4 HOH B 68 814 814 HOH HOH . H 4 HOH B 69 815 815 HOH HOH . H 4 HOH B 70 816 816 HOH HOH . H 4 HOH B 71 817 817 HOH HOH . H 4 HOH B 72 818 818 HOH HOH . H 4 HOH B 73 819 819 HOH HOH . H 4 HOH B 74 820 820 HOH HOH . H 4 HOH B 75 821 821 HOH HOH . H 4 HOH B 76 822 822 HOH HOH . H 4 HOH B 77 823 823 HOH HOH . H 4 HOH B 78 825 825 HOH HOH . H 4 HOH B 79 826 826 HOH HOH . H 4 HOH B 80 827 827 HOH HOH . H 4 HOH B 81 829 829 HOH HOH . H 4 HOH B 82 830 830 HOH HOH . H 4 HOH B 83 831 831 HOH HOH . H 4 HOH B 84 841 841 HOH HOH . H 4 HOH B 85 847 847 HOH HOH . H 4 HOH B 86 902 902 HOH HOH . H 4 HOH B 87 905 905 HOH HOH . H 4 HOH B 88 907 907 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 UMP . . . E 2 44.441 33.864 24.974 1 31.38 ? N1 UMP 567 B 1 HETATM 2 C C2 UMP . . . E 2 43.816 34.93 25.628 1 30.17 ? C2 UMP 567 B 1 HETATM 3 N N3 UMP . . . E 2 42.929 35.696 24.92 1 34.21 ? N3 UMP 567 B 1 HETATM 4 C C4 UMP . . . E 2 42.586 35.501 23.607 1 37.09 ? C4 UMP 567 B 1 HETATM 5 C C5 UMP . . . E 2 43.205 34.324 22.852 1 34.42 ? C5 UMP 567 B 1 HETATM 6 C C6 UMP . . . E 2 43.966 33.239 23.696 1 31.75 ? C6 UMP 567 B 1 HETATM 7 O O2 UMP . . . E 2 44.024 35.22 26.804 1 29.79 ? O2 UMP 567 B 1 HETATM 8 O O4 UMP . . . E 2 41.748 36.233 23.082 1 41.72 ? O4 UMP 567 B 1 HETATM 9 C C1' UMP . . . E 2 45.686 33.331 25.558 1 30.64 ? C1' UMP 567 B 1 HETATM 10 C C2' UMP . . . E 2 45.453 32.056 26.362 1 31.55 ? C2' UMP 567 B 1 HETATM 11 C C3' UMP . . . E 2 46.848 31.465 26.498 1 31.83 ? C3' UMP 567 B 1 HETATM 12 C C4' UMP . . . E 2 47.299 31.644 25.027 1 30.46 ? C4' UMP 567 B 1 HETATM 13 O O3' UMP . . . E 2 47.637 32.284 27.382 1 24.82 ? O3' UMP 567 B 1 HETATM 14 O O4' UMP . . . E 2 46.743 32.947 24.622 1 31.31 ? O4' UMP 567 B 1 HETATM 15 C C5' UMP . . . E 2 46.724 30.587 24.049 1 32 ? C5' UMP 567 B 1 HETATM 16 O O5' UMP . . . E 2 47.382 29.286 24.186 1 29.31 ? O5' UMP 567 B 1 HETATM 17 P P UMP . . . E 2 46.721 28.003 24.869 1 24.91 ? P UMP 567 B 1 HETATM 18 O OP1 UMP . . . E 2 47.79 27.126 25.407 1 24.39 ? OP1 UMP 567 B 1 HETATM 19 O OP2 UMP . . . E 2 45.822 28.387 25.985 1 22.05 ? OP2 UMP 567 B 1 HETATM 20 O OP3 UMP . . . E 2 45.986 27.229 23.847 1 13.38 ? OP3 UMP 567 B 1 HETATM 21 H HN3 UMP . . . E 2 42.543 36.487 25.353 1 15 ? HN3 UMP 567 B 1 # _model_server_stats.io_time_ms 79 _model_server_stats.parse_time_ms 82 _model_server_stats.create_model_time_ms 90 _model_server_stats.query_time_ms 503 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 21 #