data_1EMJ # _model_server_result.job_id TUajMNzUwgfnnuUtnIoGyQ _model_server_result.datetime_utc '2024-12-26 12:55:31' _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 1emj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":55}' # _entry.id 1EMJ # _exptl.entry_id 1EMJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 112.087 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URACIL _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 1EMJ _cell.length_a 48.554 _cell.length_b 64.853 _cell.length_c 96.01 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1EMJ _symmetry.cell_setting orthorhombic _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 ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 D _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 covale ? covale1 A O3' DT 3 B DT 4 1_555 A P ASU 4 B ASU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? covale ? covale2 A O3' ASU 4 B ASU 5 1_555 A P DA 5 B DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? hydrog 'DT-DA PAIR' hydrog1 A O4 DT 1 B DT 2 1_555 B N6 DA 10 C DA 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N1 DG 2 B DG 3 1_555 B N3 DC 9 C DC 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N2 DG 2 B DG 3 1_555 B O2 DC 9 C DC 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A O6 DG 2 B DG 3 1_555 B N4 DC 9 C DC 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N3 DT 3 B DT 4 1_555 B N1 DA 8 C DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O4 DT 3 B DT 4 1_555 B N6 DA 8 C DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DA 5 B DA 6 1_555 B N3 DT 6 C DT 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N6 DA 5 B DA 6 1_555 B O4 DT 6 C DT 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 DT 6 B DT 7 1_555 B N1 DA 5 C DA 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O4 DT 6 B DT 7 1_555 B N6 DA 5 C DA 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 DC 7 B DC 8 1_555 B N1 DG 4 C DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N4 DC 7 B DC 8 1_555 B O6 DG 4 C DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O2 DC 7 B DC 8 1_555 B N2 DG 4 C DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N3 DT 8 B DT 9 1_555 B N1 DA 3 C DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O4 DT 8 B DT 9 1_555 B N6 DA 3 C DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 DT 9 B DT 10 1_555 B N1 DA 2 C DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O4 DT 9 B DT 10 1_555 B N6 DA 2 C DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C4 H4 N2 O2' _chem_comp.formula_weight 112.087 _chem_comp.id URA _chem_comp.mon_nstd_flag . _chem_comp.name URACIL _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 N1 C2 URA sing 531 n n N1 C6 URA sing 532 n n N1 HN1 URA sing 533 n n C2 O2 URA doub 534 n n C2 N3 URA sing 535 n n N3 C4 URA sing 536 n n N3 HN3 URA sing 537 n n C4 O4 URA doub 538 n n C4 C5 URA sing 539 n n C5 C6 URA doub 540 n n C5 H5 URA sing 541 n n C6 H6 URA sing 542 n n # _atom_sites.entry_id 1EMJ _atom_sites.fract_transf_matrix[1][1] 0.020596 _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] 0.015419 _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] 0.010416 _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 D 4 URA A 1 55 55 URA URA . E 5 HOH B 1 535 535 HOH HOH . E 5 HOH B 2 536 536 HOH HOH . E 5 HOH B 3 540 540 HOH HOH . E 5 HOH B 4 573 573 HOH HOH . E 5 HOH B 5 574 574 HOH HOH . E 5 HOH B 6 752 752 HOH HOH . E 5 HOH B 7 753 753 HOH HOH . E 5 HOH B 8 771 771 HOH HOH . E 5 HOH B 9 772 772 HOH HOH . E 5 HOH B 10 774 774 HOH HOH . E 5 HOH B 11 778 778 HOH HOH . E 5 HOH B 12 789 789 HOH HOH . F 5 HOH C 1 564 564 HOH HOH . F 5 HOH C 2 577 577 HOH HOH . F 5 HOH C 3 587 587 HOH HOH . F 5 HOH C 4 756 756 HOH HOH . F 5 HOH C 5 773 773 HOH HOH . G 5 HOH A 1 400 400 HOH HOH . G 5 HOH A 2 403 403 HOH HOH . G 5 HOH A 3 404 404 HOH HOH . G 5 HOH A 4 405 405 HOH HOH . G 5 HOH A 5 406 406 HOH HOH . G 5 HOH A 6 408 408 HOH HOH . G 5 HOH A 7 409 409 HOH HOH . G 5 HOH A 8 411 411 HOH HOH . G 5 HOH A 9 420 420 HOH HOH . G 5 HOH A 10 421 421 HOH HOH . G 5 HOH A 11 422 422 HOH HOH . G 5 HOH A 12 427 427 HOH HOH . G 5 HOH A 13 429 429 HOH HOH . G 5 HOH A 14 430 430 HOH HOH . G 5 HOH A 15 431 431 HOH HOH . G 5 HOH A 16 432 432 HOH HOH . G 5 HOH A 17 433 433 HOH HOH . G 5 HOH A 18 435 435 HOH HOH . G 5 HOH A 19 438 438 HOH HOH . G 5 HOH A 20 439 439 HOH HOH . G 5 HOH A 21 441 441 HOH HOH . G 5 HOH A 22 450 450 HOH HOH . G 5 HOH A 23 452 452 HOH HOH . G 5 HOH A 24 464 464 HOH HOH . G 5 HOH A 25 473 473 HOH HOH . G 5 HOH A 26 474 474 HOH HOH . G 5 HOH A 27 477 477 HOH HOH . G 5 HOH A 28 478 478 HOH HOH . G 5 HOH A 29 521 521 HOH HOH . G 5 HOH A 30 522 522 HOH HOH . G 5 HOH A 31 523 523 HOH HOH . G 5 HOH A 32 524 524 HOH HOH . G 5 HOH A 33 525 525 HOH HOH . G 5 HOH A 34 527 527 HOH HOH . G 5 HOH A 35 531 531 HOH HOH . G 5 HOH A 36 534 534 HOH HOH . G 5 HOH A 37 543 543 HOH HOH . G 5 HOH A 38 544 544 HOH HOH . G 5 HOH A 39 548 548 HOH HOH . G 5 HOH A 40 549 549 HOH HOH . G 5 HOH A 41 551 551 HOH HOH . G 5 HOH A 42 556 556 HOH HOH . G 5 HOH A 43 559 559 HOH HOH . G 5 HOH A 44 560 560 HOH HOH . G 5 HOH A 45 563 563 HOH HOH . G 5 HOH A 46 570 570 HOH HOH . G 5 HOH A 47 575 575 HOH HOH . G 5 HOH A 48 584 584 HOH HOH . G 5 HOH A 49 589 589 HOH HOH . G 5 HOH A 50 596 596 HOH HOH . G 5 HOH A 51 597 597 HOH HOH . G 5 HOH A 52 598 598 HOH HOH . G 5 HOH A 53 599 599 HOH HOH . G 5 HOH A 54 601 601 HOH HOH . G 5 HOH A 55 700 700 HOH HOH . G 5 HOH A 56 702 702 HOH HOH . G 5 HOH A 57 704 704 HOH HOH . G 5 HOH A 58 705 705 HOH HOH . G 5 HOH A 59 706 706 HOH HOH . G 5 HOH A 60 708 708 HOH HOH . G 5 HOH A 61 709 709 HOH HOH . G 5 HOH A 62 711 711 HOH HOH . G 5 HOH A 63 712 712 HOH HOH . G 5 HOH A 64 714 714 HOH HOH . G 5 HOH A 65 716 716 HOH HOH . G 5 HOH A 66 717 717 HOH HOH . G 5 HOH A 67 718 718 HOH HOH . G 5 HOH A 68 750 750 HOH HOH . G 5 HOH A 69 751 751 HOH HOH . G 5 HOH A 70 754 754 HOH HOH . G 5 HOH A 71 755 755 HOH HOH . G 5 HOH A 72 757 757 HOH HOH . G 5 HOH A 73 758 758 HOH HOH . G 5 HOH A 74 759 759 HOH HOH . G 5 HOH A 75 760 760 HOH HOH . G 5 HOH A 76 761 761 HOH HOH . G 5 HOH A 77 762 762 HOH HOH . G 5 HOH A 78 763 763 HOH HOH . G 5 HOH A 79 764 764 HOH HOH . G 5 HOH A 80 766 766 HOH HOH . G 5 HOH A 81 767 767 HOH HOH . G 5 HOH A 82 768 768 HOH HOH . G 5 HOH A 83 769 769 HOH HOH . G 5 HOH A 84 770 770 HOH HOH . G 5 HOH A 85 776 776 HOH HOH . G 5 HOH A 86 777 777 HOH HOH . G 5 HOH A 87 779 779 HOH HOH . G 5 HOH A 88 780 780 HOH HOH . G 5 HOH A 89 781 781 HOH HOH . G 5 HOH A 90 782 782 HOH HOH . G 5 HOH A 91 783 783 HOH HOH . G 5 HOH A 92 790 790 HOH HOH . G 5 HOH A 93 791 791 HOH HOH . G 5 HOH A 94 792 792 HOH HOH . G 5 HOH A 95 793 793 HOH HOH . G 5 HOH A 96 794 794 HOH HOH . G 5 HOH A 97 795 795 HOH HOH . G 5 HOH A 98 796 796 HOH HOH . G 5 HOH A 99 799 799 HOH HOH . G 5 HOH A 100 800 800 HOH HOH . G 5 HOH A 101 801 801 HOH HOH . G 5 HOH A 102 802 802 HOH HOH . G 5 HOH A 103 804 804 HOH HOH . G 5 HOH A 104 805 805 HOH HOH . G 5 HOH A 105 806 806 HOH HOH . G 5 HOH A 106 808 808 HOH HOH . G 5 HOH A 107 809 809 HOH HOH . G 5 HOH A 108 810 810 HOH HOH . G 5 HOH A 109 811 811 HOH HOH . G 5 HOH A 110 812 812 HOH HOH . G 5 HOH A 111 813 813 HOH HOH . G 5 HOH A 112 814 814 HOH HOH . G 5 HOH A 113 815 815 HOH HOH . G 5 HOH A 114 816 816 HOH HOH . G 5 HOH A 115 817 817 HOH HOH . G 5 HOH A 116 818 818 HOH HOH . G 5 HOH A 117 819 819 HOH HOH . G 5 HOH A 118 820 820 HOH HOH . G 5 HOH A 119 821 821 HOH HOH . G 5 HOH A 120 822 822 HOH HOH . G 5 HOH A 121 823 823 HOH HOH . G 5 HOH A 122 824 824 HOH HOH . G 5 HOH A 123 825 825 HOH HOH . G 5 HOH A 124 826 826 HOH HOH . G 5 HOH A 125 827 827 HOH HOH . G 5 HOH A 126 828 828 HOH HOH . G 5 HOH A 127 829 829 HOH HOH . G 5 HOH A 128 830 830 HOH HOH . G 5 HOH A 129 831 831 HOH HOH . G 5 HOH A 130 832 832 HOH HOH . G 5 HOH A 131 833 833 HOH HOH . G 5 HOH A 132 834 834 HOH HOH . G 5 HOH A 133 835 835 HOH HOH . G 5 HOH A 134 836 836 HOH HOH . G 5 HOH A 135 837 837 HOH HOH . G 5 HOH A 136 838 838 HOH HOH . G 5 HOH A 137 839 839 HOH HOH . G 5 HOH A 138 840 840 HOH HOH . G 5 HOH A 139 841 841 HOH HOH . G 5 HOH A 140 844 844 HOH HOH . G 5 HOH A 141 845 845 HOH HOH . G 5 HOH A 142 846 846 HOH HOH . G 5 HOH A 143 847 847 HOH HOH . G 5 HOH A 144 848 848 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 URA . . . D 4 17.696 2.464 8.25 1 23.18 ? N1 URA 55 A 1 HETATM 2 C C2 URA . . . D 4 17.48 2.414 6.886 1 22.82 ? C2 URA 55 A 1 HETATM 3 O O2 URA . . . D 4 16.383 2.218 6.405 1 22.87 ? O2 URA 55 A 1 HETATM 4 N N3 URA . . . D 4 18.599 2.612 6.112 1 22.18 ? N3 URA 55 A 1 HETATM 5 C C4 URA . . . D 4 19.883 2.868 6.562 1 22.87 ? C4 URA 55 A 1 HETATM 6 O O4 URA . . . D 4 20.786 3.077 5.752 1 21.75 ? O4 URA 55 A 1 HETATM 7 C C5 URA . . . D 4 20.013 2.915 7.981 1 22.91 ? C5 URA 55 A 1 HETATM 8 C C6 URA . . . D 4 18.943 2.713 8.757 1 23.36 ? C6 URA 55 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 8 #