data_8Z31 # _model_server_result.job_id x0XBLSIfDBAQmkIyxs5jRg _model_server_result.datetime_utc '2025-07-03 23:16:48' _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 8z31 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":504}' # _entry.id 8Z31 # _exptl.entry_id 8Z31 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 225.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[(2,6-dimethyl-5-oxidanyl-pyrimidin-4-yl)carbonylamino]ethanoic acid' _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 8Z31 _cell.length_a 71.627 _cell.length_b 71.627 _cell.length_c 45.402 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Z31 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _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 5 _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 NE2 HIS 134 A HIS 313 1_555 B FE FE2 . A FE2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc2 A OD2 ASP 136 A ASP 315 1_555 B FE FE2 . A FE2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc3 A NE2 HIS 195 A HIS 374 1_555 B FE FE2 . A FE2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc4 B FE FE2 . A FE2 501 1_555 E O2 A1L0U . A A1L0U 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc5 B FE FE2 . A FE2 501 1_555 E N2 A1L0U . A A1L0U 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc6 B FE FE2 . A FE2 501 1_555 F O HOH . A HOH 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? # _chem_comp.formula 'C9 H11 N3 O4' _chem_comp.formula_weight 225.201 _chem_comp.id A1L0U _chem_comp.mon_nstd_flag . _chem_comp.name '2-[(2,6-dimethyl-5-oxidanyl-pyrimidin-4-yl)carbonylamino]ethanoic acid' _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 C6 C1 A1L0U sing 1 n n C1 N2 A1L0U doub 2 n y C1 N1 A1L0U sing 3 n y N2 C2 A1L0U sing 4 n y N1 C4 A1L0U doub 5 n y O2 C7 A1L0U doub 6 n n C2 C7 A1L0U sing 7 n n C2 C3 A1L0U doub 8 n y C4 C3 A1L0U sing 9 n y C4 C5 A1L0U sing 10 n n C7 N3 A1L0U sing 11 n n C3 O1 A1L0U sing 12 n n N3 C8 A1L0U sing 13 n n C8 C9 A1L0U sing 14 n n C9 O4 A1L0U doub 15 n n C9 O3 A1L0U sing 16 n n C5 H1 A1L0U sing 17 n n C5 H2 A1L0U sing 18 n n C5 H3 A1L0U sing 19 n n C6 H4 A1L0U sing 20 n n C6 H5 A1L0U sing 21 n n C6 H6 A1L0U sing 22 n n O3 H7 A1L0U sing 23 n n O1 H8 A1L0U sing 24 n n C8 H9 A1L0U sing 25 n n N3 H10 A1L0U sing 26 n n C8 H11 A1L0U sing 27 n n # _atom_sites.entry_id 8Z31 _atom_sites.fract_transf_matrix[1][1] 0.013961 _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] 0.013961 _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] 0.022025 _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 FE2 A 1 501 1 FE2 FE2 . C 3 SO4 A 1 502 1 SO4 SO4 . D 4 CL A 1 503 1 CL CL . E 5 A1L0U A 1 504 1 A1L0U IN1 . F 6 HOH A 1 601 57 HOH HOH . F 6 HOH A 2 602 135 HOH HOH . F 6 HOH A 3 603 16 HOH HOH . F 6 HOH A 4 604 22 HOH HOH . F 6 HOH A 5 605 90 HOH HOH . F 6 HOH A 6 606 14 HOH HOH . F 6 HOH A 7 607 117 HOH HOH . F 6 HOH A 8 608 69 HOH HOH . F 6 HOH A 9 609 8 HOH HOH . F 6 HOH A 10 610 36 HOH HOH . F 6 HOH A 11 611 63 HOH HOH . F 6 HOH A 12 612 59 HOH HOH . F 6 HOH A 13 613 12 HOH HOH . F 6 HOH A 14 614 70 HOH HOH . F 6 HOH A 15 615 76 HOH HOH . F 6 HOH A 16 616 122 HOH HOH . F 6 HOH A 17 617 11 HOH HOH . F 6 HOH A 18 618 79 HOH HOH . F 6 HOH A 19 619 102 HOH HOH . F 6 HOH A 20 620 2 HOH HOH . F 6 HOH A 21 621 32 HOH HOH . F 6 HOH A 22 622 75 HOH HOH . F 6 HOH A 23 623 21 HOH HOH . F 6 HOH A 24 624 1 HOH HOH . F 6 HOH A 25 625 5 HOH HOH . F 6 HOH A 26 626 64 HOH HOH . F 6 HOH A 27 627 35 HOH HOH . F 6 HOH A 28 628 4 HOH HOH . F 6 HOH A 29 629 86 HOH HOH . F 6 HOH A 30 630 51 HOH HOH . F 6 HOH A 31 631 44 HOH HOH . F 6 HOH A 32 632 41 HOH HOH . F 6 HOH A 33 633 141 HOH HOH . F 6 HOH A 34 634 3 HOH HOH . F 6 HOH A 35 635 27 HOH HOH . F 6 HOH A 36 636 29 HOH HOH . F 6 HOH A 37 637 58 HOH HOH . F 6 HOH A 38 638 119 HOH HOH . F 6 HOH A 39 639 47 HOH HOH . F 6 HOH A 40 640 9 HOH HOH . F 6 HOH A 41 641 28 HOH HOH . F 6 HOH A 42 642 56 HOH HOH . F 6 HOH A 43 643 43 HOH HOH . F 6 HOH A 44 644 108 HOH HOH . F 6 HOH A 45 645 65 HOH HOH . F 6 HOH A 46 646 15 HOH HOH . F 6 HOH A 47 647 116 HOH HOH . F 6 HOH A 48 648 46 HOH HOH . F 6 HOH A 49 649 45 HOH HOH . F 6 HOH A 50 650 49 HOH HOH . F 6 HOH A 51 651 103 HOH HOH . F 6 HOH A 52 652 81 HOH HOH . F 6 HOH A 53 653 38 HOH HOH . F 6 HOH A 54 654 67 HOH HOH . F 6 HOH A 55 655 62 HOH HOH . F 6 HOH A 56 656 60 HOH HOH . F 6 HOH A 57 657 78 HOH HOH . F 6 HOH A 58 658 77 HOH HOH . F 6 HOH A 59 659 53 HOH HOH . F 6 HOH A 60 660 52 HOH HOH . F 6 HOH A 61 661 118 HOH HOH . F 6 HOH A 62 662 66 HOH HOH . F 6 HOH A 63 663 13 HOH HOH . F 6 HOH A 64 664 19 HOH HOH . F 6 HOH A 65 665 80 HOH HOH . F 6 HOH A 66 666 40 HOH HOH . F 6 HOH A 67 667 120 HOH HOH . F 6 HOH A 68 668 68 HOH HOH . F 6 HOH A 69 669 37 HOH HOH . F 6 HOH A 70 670 89 HOH HOH . F 6 HOH A 71 671 30 HOH HOH . F 6 HOH A 72 672 42 HOH HOH . F 6 HOH A 73 673 55 HOH HOH . F 6 HOH A 74 674 34 HOH HOH . F 6 HOH A 75 675 139 HOH HOH . F 6 HOH A 76 676 33 HOH HOH . F 6 HOH A 77 677 31 HOH HOH . F 6 HOH A 78 678 98 HOH HOH . F 6 HOH A 79 679 50 HOH HOH . F 6 HOH A 80 680 140 HOH HOH . F 6 HOH A 81 681 73 HOH HOH . F 6 HOH A 82 682 18 HOH HOH . F 6 HOH A 83 683 24 HOH HOH . F 6 HOH A 84 684 61 HOH HOH . F 6 HOH A 85 685 132 HOH HOH . F 6 HOH A 86 686 17 HOH HOH . F 6 HOH A 87 687 6 HOH HOH . F 6 HOH A 88 688 23 HOH HOH . F 6 HOH A 89 689 92 HOH HOH . F 6 HOH A 90 690 39 HOH HOH . F 6 HOH A 91 691 133 HOH HOH . F 6 HOH A 92 692 48 HOH HOH . F 6 HOH A 93 693 71 HOH HOH . F 6 HOH A 94 694 10 HOH HOH . F 6 HOH A 95 695 25 HOH HOH . F 6 HOH A 96 696 7 HOH HOH . F 6 HOH A 97 697 20 HOH HOH . F 6 HOH A 98 698 74 HOH HOH . F 6 HOH A 99 699 104 HOH HOH . F 6 HOH A 100 700 113 HOH HOH . F 6 HOH A 101 701 115 HOH HOH . F 6 HOH A 102 702 26 HOH HOH . F 6 HOH A 103 703 124 HOH HOH . F 6 HOH A 104 704 54 HOH HOH . F 6 HOH A 105 705 137 HOH HOH . F 6 HOH A 106 706 109 HOH HOH . F 6 HOH A 107 707 91 HOH HOH . F 6 HOH A 108 708 121 HOH HOH . F 6 HOH A 109 709 85 HOH HOH . F 6 HOH A 110 710 112 HOH HOH . F 6 HOH A 111 711 110 HOH HOH . F 6 HOH A 112 712 72 HOH HOH . F 6 HOH A 113 713 138 HOH HOH . F 6 HOH A 114 714 87 HOH HOH . F 6 HOH A 115 715 83 HOH HOH . F 6 HOH A 116 716 94 HOH HOH . F 6 HOH A 117 717 107 HOH HOH . F 6 HOH A 118 718 130 HOH HOH . F 6 HOH A 119 719 128 HOH HOH . F 6 HOH A 120 720 100 HOH HOH . F 6 HOH A 121 721 93 HOH HOH . F 6 HOH A 122 722 99 HOH HOH . F 6 HOH A 123 723 142 HOH HOH . F 6 HOH A 124 724 127 HOH HOH . F 6 HOH A 125 725 134 HOH HOH . F 6 HOH A 126 726 125 HOH HOH . F 6 HOH A 127 727 105 HOH HOH . F 6 HOH A 128 728 114 HOH HOH . F 6 HOH A 129 729 131 HOH HOH . F 6 HOH A 130 730 123 HOH HOH . F 6 HOH A 131 731 84 HOH HOH . F 6 HOH A 132 732 106 HOH HOH . F 6 HOH A 133 733 126 HOH HOH . F 6 HOH A 134 734 129 HOH HOH . F 6 HOH A 135 735 136 HOH HOH . F 6 HOH A 136 736 111 HOH HOH . F 6 HOH A 137 737 97 HOH HOH . F 6 HOH A 138 738 95 HOH HOH . F 6 HOH A 139 739 96 HOH HOH . F 6 HOH A 140 740 101 HOH HOH . F 6 HOH A 141 741 82 HOH HOH . F 6 HOH A 142 742 88 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 C7 A1L0U . . . E 5 13.817 26.251 -1.917 1 32.93 ? C7 A1L0U 504 A 1 HETATM 2 C C1 A1L0U . . . E 5 14.71 23.522 -4.157 1 34.79 ? C1 A1L0U 504 A 1 HETATM 3 C C2 A1L0U . . . E 5 14.546 25.062 -2.461 1 33.39 ? C2 A1L0U 504 A 1 HETATM 4 C C3 A1L0U . . . E 5 15.588 24.457 -1.811 1 34.79 ? C3 A1L0U 504 A 1 HETATM 5 C C4 A1L0U . . . E 5 16.189 23.378 -2.399 1 34.92 ? C4 A1L0U 504 A 1 HETATM 6 C C5 A1L0U . . . E 5 17.349 22.676 -1.761 1 35.94 ? C5 A1L0U 504 A 1 HETATM 7 C C6 A1L0U . . . E 5 14.234 22.981 -5.468 1 35.13 ? C6 A1L0U 504 A 1 HETATM 8 O O2 A1L0U . . . E 5 13.033 26.835 -2.656 1 31.45 ? O2 A1L0U 504 A 1 HETATM 9 O O3 A1L0U . . . E 5 14.394 27.019 2.063 1 27.94 ? O3 A1L0U 504 A 1 HETATM 10 O O4 A1L0U . . . E 5 13.061 28.799 2.053 1 27.19 ? O4 A1L0U 504 A 1 HETATM 11 O O1 A1L0U . . . E 5 16.1 24.877 -0.623 1 36.85 ? O1 A1L0U 504 A 1 HETATM 12 N N1 A1L0U . . . E 5 15.743 22.906 -3.573 1 34.52 ? N1 A1L0U 504 A 1 HETATM 13 N N2 A1L0U . . . E 5 14.071 24.587 -3.657 1 32.32 ? N2 A1L0U 504 A 1 HETATM 14 N N3 A1L0U . . . E 5 14.013 26.54 -0.627 1 32.51 ? N3 A1L0U 504 A 1 HETATM 15 C C8 A1L0U . . . E 5 13.235 27.557 0.049 1 30.33 ? C8 A1L0U 504 A 1 HETATM 16 C C9 A1L0U . . . E 5 13.595 27.806 1.509 1 29.15 ? C9 A1L0U 504 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #