data_5JAN # _model_server_result.job_id i_0uUPPOdtE3sSTLHXNBbQ _model_server_result.datetime_utc '2025-01-25 11:29:34' _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 5jan # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":504}' # _entry.id 5JAN # _exptl.entry_id 5JAN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 212.246 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,3-dimethyl-6-(2-methylpropoxy)pyrimidine-2,4(1H,3H)-dione _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 112.6 _cell.angle_gamma 90 _cell.entry_id 5JAN _cell.length_a 100.373 _cell.length_b 92.08 _cell.length_c 48.273 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JAN _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 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 _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 4 _struct_asym.id E _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 metalc ? metalc1 A O GLU 240 A GLU 285 1_555 D CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc2 A O GLU 240 A GLU 285 1_555 D CA CA . A CA 503 2_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc3 D CA CA . A CA 503 1_555 F O HOH . A HOH 678 2_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc4 D CA CA . A CA 503 1_555 F O HOH . A HOH 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc5 D CA CA . A CA 503 1_555 F O HOH . A HOH 719 2_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? # _chem_comp.formula 'C10 H16 N2 O3' _chem_comp.formula_weight 212.246 _chem_comp.id 6HP _chem_comp.mon_nstd_flag . _chem_comp.name 1,3-dimethyl-6-(2-methylpropoxy)pyrimidine-2,4(1H,3H)-dione _chem_comp.type non-polymer _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 C3 C2 6HP sing 1 n n C2 C1 6HP sing 2 n n C2 C4 6HP sing 3 n n O5 C4 6HP sing 4 n n O5 C6 6HP sing 5 n n C7 C6 6HP doub 6 n n C7 C8 6HP sing 7 n n C6 N14 6HP sing 8 n n O9 C8 6HP doub 9 n n C8 N10 6HP sing 10 n n N14 C15 6HP sing 11 n n N14 C12 6HP sing 12 n n N10 C12 6HP sing 13 n n N10 C11 6HP sing 14 n n C12 O13 6HP doub 15 n n C1 H18 6HP sing 16 n n C1 H17 6HP sing 17 n n C1 H16 6HP sing 18 n n C2 H19 6HP sing 19 n n C3 H22 6HP sing 20 n n C3 H21 6HP sing 21 n n C3 H20 6HP sing 22 n n C7 H25 6HP sing 23 n n C11 H27 6HP sing 24 n n C11 H28 6HP sing 25 n n C11 H26 6HP sing 26 n n C15 H31 6HP sing 27 n n C15 H30 6HP sing 28 n n C15 H29 6HP sing 29 n n C4 H23 6HP sing 30 n n C4 H24 6HP sing 31 n n # _atom_sites.entry_id 5JAN _atom_sites.fract_transf_matrix[1][1] 0.009963 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004147 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01086 _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] 0.022438 _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 CL A 1 501 133 CL CL . C 2 CL A 1 502 134 CL CL . D 3 CA A 1 503 1 CA CA . E 4 6HP A 1 504 1 6HP L01 . F 5 HOH A 1 601 37 HOH HOH . F 5 HOH A 2 602 119 HOH HOH . F 5 HOH A 3 603 35 HOH HOH . F 5 HOH A 4 604 55 HOH HOH . F 5 HOH A 5 605 13 HOH HOH . F 5 HOH A 6 606 1 HOH HOH . F 5 HOH A 7 607 44 HOH HOH . F 5 HOH A 8 608 131 HOH HOH . F 5 HOH A 9 609 124 HOH HOH . F 5 HOH A 10 610 47 HOH HOH . F 5 HOH A 11 611 69 HOH HOH . F 5 HOH A 12 612 85 HOH HOH . F 5 HOH A 13 613 30 HOH HOH . F 5 HOH A 14 614 130 HOH HOH . F 5 HOH A 15 615 129 HOH HOH . F 5 HOH A 16 616 3 HOH HOH . F 5 HOH A 17 617 114 HOH HOH . F 5 HOH A 18 618 34 HOH HOH . F 5 HOH A 19 619 53 HOH HOH . F 5 HOH A 20 620 29 HOH HOH . F 5 HOH A 21 621 40 HOH HOH . F 5 HOH A 22 622 11 HOH HOH . F 5 HOH A 23 623 63 HOH HOH . F 5 HOH A 24 624 48 HOH HOH . F 5 HOH A 25 625 25 HOH HOH . F 5 HOH A 26 626 73 HOH HOH . F 5 HOH A 27 627 16 HOH HOH . F 5 HOH A 28 628 52 HOH HOH . F 5 HOH A 29 629 93 HOH HOH . F 5 HOH A 30 630 15 HOH HOH . F 5 HOH A 31 631 6 HOH HOH . F 5 HOH A 32 632 4 HOH HOH . F 5 HOH A 33 633 132 HOH HOH . F 5 HOH A 34 634 57 HOH HOH . F 5 HOH A 35 635 9 HOH HOH . F 5 HOH A 36 636 107 HOH HOH . F 5 HOH A 37 637 88 HOH HOH . F 5 HOH A 38 638 64 HOH HOH . F 5 HOH A 39 639 109 HOH HOH . F 5 HOH A 40 640 104 HOH HOH . F 5 HOH A 41 641 8 HOH HOH . F 5 HOH A 42 642 65 HOH HOH . F 5 HOH A 43 643 105 HOH HOH . F 5 HOH A 44 644 5 HOH HOH . F 5 HOH A 45 645 112 HOH HOH . F 5 HOH A 46 646 62 HOH HOH . F 5 HOH A 47 647 50 HOH HOH . F 5 HOH A 48 648 103 HOH HOH . F 5 HOH A 49 649 71 HOH HOH . F 5 HOH A 50 650 3 HOH HOH . F 5 HOH A 51 651 94 HOH HOH . F 5 HOH A 52 652 81 HOH HOH . F 5 HOH A 53 653 56 HOH HOH . F 5 HOH A 54 654 123 HOH HOH . F 5 HOH A 55 655 68 HOH HOH . F 5 HOH A 56 656 10 HOH HOH . F 5 HOH A 57 657 70 HOH HOH . F 5 HOH A 58 658 95 HOH HOH . F 5 HOH A 59 659 49 HOH HOH . F 5 HOH A 60 660 46 HOH HOH . F 5 HOH A 61 661 42 HOH HOH . F 5 HOH A 62 662 101 HOH HOH . F 5 HOH A 63 663 41 HOH HOH . F 5 HOH A 64 664 38 HOH HOH . F 5 HOH A 65 665 92 HOH HOH . F 5 HOH A 66 666 78 HOH HOH . F 5 HOH A 67 667 45 HOH HOH . F 5 HOH A 68 668 19 HOH HOH . F 5 HOH A 69 669 121 HOH HOH . F 5 HOH A 70 670 26 HOH HOH . F 5 HOH A 71 671 39 HOH HOH . F 5 HOH A 72 672 120 HOH HOH . F 5 HOH A 73 673 31 HOH HOH . F 5 HOH A 74 674 127 HOH HOH . F 5 HOH A 75 675 17 HOH HOH . F 5 HOH A 76 676 28 HOH HOH . F 5 HOH A 77 677 82 HOH HOH . F 5 HOH A 78 678 59 HOH HOH . F 5 HOH A 79 679 14 HOH HOH . F 5 HOH A 80 680 96 HOH HOH . F 5 HOH A 81 681 110 HOH HOH . F 5 HOH A 82 682 22 HOH HOH . F 5 HOH A 83 683 18 HOH HOH . F 5 HOH A 84 684 2 HOH HOH . F 5 HOH A 85 685 116 HOH HOH . F 5 HOH A 86 686 87 HOH HOH . F 5 HOH A 87 687 91 HOH HOH . F 5 HOH A 88 688 117 HOH HOH . F 5 HOH A 89 689 33 HOH HOH . F 5 HOH A 90 690 24 HOH HOH . F 5 HOH A 91 691 106 HOH HOH . F 5 HOH A 92 692 27 HOH HOH . F 5 HOH A 93 693 43 HOH HOH . F 5 HOH A 94 694 128 HOH HOH . F 5 HOH A 95 695 80 HOH HOH . F 5 HOH A 96 696 21 HOH HOH . F 5 HOH A 97 697 36 HOH HOH . F 5 HOH A 98 698 67 HOH HOH . F 5 HOH A 99 699 54 HOH HOH . F 5 HOH A 100 700 72 HOH HOH . F 5 HOH A 101 701 75 HOH HOH . F 5 HOH A 102 702 76 HOH HOH . F 5 HOH A 103 703 51 HOH HOH . F 5 HOH A 104 704 23 HOH HOH . F 5 HOH A 105 705 66 HOH HOH . F 5 HOH A 106 706 108 HOH HOH . F 5 HOH A 107 707 122 HOH HOH . F 5 HOH A 108 708 20 HOH HOH . F 5 HOH A 109 709 60 HOH HOH . F 5 HOH A 110 710 12 HOH HOH . F 5 HOH A 111 711 100 HOH HOH . F 5 HOH A 112 712 32 HOH HOH . F 5 HOH A 113 713 118 HOH HOH . F 5 HOH A 114 714 79 HOH HOH . F 5 HOH A 115 715 102 HOH HOH . F 5 HOH A 116 716 77 HOH HOH . F 5 HOH A 117 717 98 HOH HOH . F 5 HOH A 118 718 97 HOH HOH . F 5 HOH A 119 719 1 HOH HOH . F 5 HOH A 120 720 86 HOH HOH . F 5 HOH A 121 721 115 HOH HOH . F 5 HOH A 122 722 61 HOH HOH . F 5 HOH A 123 723 90 HOH HOH . F 5 HOH A 124 724 126 HOH HOH . F 5 HOH A 125 725 99 HOH HOH . F 5 HOH A 126 726 7 HOH HOH . F 5 HOH A 127 727 83 HOH HOH . F 5 HOH A 128 728 125 HOH HOH . F 5 HOH A 129 729 111 HOH HOH . F 5 HOH A 130 730 113 HOH HOH . F 5 HOH A 131 731 84 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 C C1 6HP . . . E 4 31.848 -5.299 -5.262 0.62 40.55 ? C1 6HP 504 A 1 HETATM 2 C C2 6HP . . . E 4 30.798 -4.326 -5.804 0.62 39.35 ? C2 6HP 504 A 1 HETATM 3 C C3 6HP . . . E 4 30.016 -4.948 -6.964 0.62 38.18 ? C3 6HP 504 A 1 HETATM 4 C C6 6HP . . . E 4 29.064 -1.776 -3.886 0.62 30.94 ? C6 6HP 504 A 1 HETATM 5 C C7 6HP . . . E 4 29.384 -0.512 -4.257 0.62 30.86 ? C7 6HP 504 A 1 HETATM 6 C C8 6HP . . . E 4 29.175 0.606 -3.392 0.62 28.48 ? C8 6HP 504 A 1 HETATM 7 O O9 6HP . . . E 4 29.446 1.766 -3.679 0.62 30.12 ? O9 6HP 504 A 1 HETATM 8 C C11 6HP . . . E 4 28.39 1.426 -1.221 0.62 27.58 ? C11 6HP 504 A 1 HETATM 9 C C12 6HP . . . E 4 28.275 -0.981 -1.715 0.62 30.74 ? C12 6HP 504 A 1 HETATM 10 C C15 6HP . . . E 4 28.148 -3.374 -2.17 0.62 34.57 ? C15 6HP 504 A 1 HETATM 11 C C4 6HP . . . E 4 29.861 -3.868 -4.69 0.62 36.73 ? C4 6HP 504 A 1 HETATM 12 O O5 6HP . . . E 4 29.411 -2.542 -4.971 0.62 33.16 ? O5 6HP 504 A 1 HETATM 13 N N10 6HP . . . E 4 28.622 0.304 -2.144 0.62 29.56 ? N10 6HP 504 A 1 HETATM 14 O O13 6HP . . . E 4 27.796 -1.178 -0.612 0.62 31.93 ? O13 6HP 504 A 1 HETATM 15 N N14 6HP . . . E 4 28.506 -2.014 -2.606 0.62 30.38 ? N14 6HP 504 A 1 HETATM 16 H H18 6HP . . . E 4 31.954 -6.044 -5.882 0.62 39.84 ? H18 6HP 504 A 1 HETATM 17 H H17 6HP . . . E 4 32.7 -4.835 -5.162 0.62 39.41 ? H17 6HP 504 A 1 HETATM 18 H H16 6HP . . . E 4 31.559 -5.639 -4.393 0.62 39.64 ? H16 6HP 504 A 1 HETATM 19 H H19 6HP . . . E 4 31.268 -3.533 -6.147 0.62 38.09 ? H19 6HP 504 A 1 HETATM 20 H H22 6HP . . . E 4 30.277 -4.516 -7.801 0.62 38.48 ? H22 6HP 504 A 1 HETATM 21 H H21 6HP . . . E 4 30.213 -5.903 -7.015 0.62 38.59 ? H21 6HP 504 A 1 HETATM 22 H H20 6HP . . . E 4 29.059 -4.821 -6.817 0.62 38.34 ? H20 6HP 504 A 1 HETATM 23 H H25 6HP . . . E 4 29.759 -0.356 -5.117 0.62 30.41 ? H25 6HP 504 A 1 HETATM 24 H H27 6HP . . . E 4 27.821 2.092 -1.654 0.62 28.61 ? H27 6HP 504 A 1 HETATM 25 H H28 6HP . . . E 4 29.244 1.833 -0.984 0.62 27.59 ? H28 6HP 504 A 1 HETATM 26 H H26 6HP . . . E 4 27.95 1.102 -0.413 0.62 28.34 ? H26 6HP 504 A 1 HETATM 27 H H31 6HP . . . E 4 27.694 -3.84 -2.897 0.62 33.55 ? H31 6HP 504 A 1 HETATM 28 H H30 6HP . . . E 4 28.957 -3.862 -1.926 0.62 33.4 ? H30 6HP 504 A 1 HETATM 29 H H29 6HP . . . E 4 27.554 -3.325 -1.397 0.62 33.22 ? H29 6HP 504 A 1 HETATM 30 H H23 6HP . . . E 4 29.093 -4.474 -4.63 0.62 36.12 ? H23 6HP 504 A 1 HETATM 31 H H24 6HP . . . E 4 30.334 -3.882 -3.831 0.62 34.68 ? H24 6HP 504 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #