data_1BID # _model_server_result.job_id OvKxsgWmBQK15ZL5oxGncg _model_server_result.datetime_utc '2024-11-05 16:37:03' _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 1bid # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":603}' # _entry.id 1BID # _exptl.entry_id 1BID _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 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 1BID _cell.length_a 133.06 _cell.length_b 133.06 _cell.length_c 133.06 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BID _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 16_555 x,-y,-z+1/2 1 0 0 0 -1 0 0 0 -1 0 0 66.53 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id C _struct_conn.ptnr1_label_comp_id FMT _struct_conn.ptnr1_label_seq_id 1 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id FMT _struct_conn.ptnr1_auth_seq_id 0 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id MET _struct_conn.ptnr2_label_seq_id 2 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id MET _struct_conn.ptnr2_auth_seq_id 1 _struct_conn.ptnr2_symmetry 1_555 _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 1.325 _struct_conn.pdbx_value_order ? # _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 # _atom_sites.entry_id 1BID _atom_sites.fract_transf_matrix[1][1] 0.007515 _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] 0.007515 _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] 0.007515 _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 UMP A 1 603 603 UMP UMP . C 3 HOH A 1 700 700 HOH HOH . C 3 HOH A 2 701 701 HOH HOH . C 3 HOH A 3 702 702 HOH HOH . C 3 HOH A 4 703 703 HOH HOH . C 3 HOH A 5 704 704 HOH HOH . C 3 HOH A 6 705 705 HOH HOH . C 3 HOH A 7 706 706 HOH HOH . C 3 HOH A 8 707 707 HOH HOH . C 3 HOH A 9 708 708 HOH HOH . C 3 HOH A 10 709 709 HOH HOH . C 3 HOH A 11 710 710 HOH HOH . C 3 HOH A 12 711 711 HOH HOH . C 3 HOH A 13 712 712 HOH HOH . C 3 HOH A 14 713 713 HOH HOH . C 3 HOH A 15 714 714 HOH HOH . C 3 HOH A 16 715 715 HOH HOH . C 3 HOH A 17 716 716 HOH HOH . C 3 HOH A 18 717 717 HOH HOH . C 3 HOH A 19 718 718 HOH HOH . C 3 HOH A 20 719 719 HOH HOH . C 3 HOH A 21 720 720 HOH HOH . C 3 HOH A 22 721 721 HOH HOH . C 3 HOH A 23 722 722 HOH HOH . C 3 HOH A 24 723 723 HOH HOH . C 3 HOH A 25 724 724 HOH HOH . C 3 HOH A 26 725 725 HOH HOH . C 3 HOH A 27 726 726 HOH HOH . C 3 HOH A 28 727 727 HOH HOH . C 3 HOH A 29 728 728 HOH HOH . C 3 HOH A 30 729 729 HOH HOH . C 3 HOH A 31 730 730 HOH HOH . C 3 HOH A 32 731 731 HOH HOH . C 3 HOH A 33 732 732 HOH HOH . C 3 HOH A 34 733 733 HOH HOH . C 3 HOH A 35 734 734 HOH HOH . C 3 HOH A 36 735 735 HOH HOH . C 3 HOH A 37 736 736 HOH HOH . C 3 HOH A 38 737 737 HOH HOH . C 3 HOH A 39 738 738 HOH HOH . C 3 HOH A 40 739 739 HOH HOH . C 3 HOH A 41 740 740 HOH HOH . C 3 HOH A 42 741 741 HOH HOH . C 3 HOH A 43 742 742 HOH HOH . C 3 HOH A 44 743 743 HOH HOH . C 3 HOH A 45 744 744 HOH HOH . C 3 HOH A 46 745 745 HOH HOH . C 3 HOH A 47 746 746 HOH HOH . C 3 HOH A 48 747 747 HOH HOH . C 3 HOH A 49 748 748 HOH HOH . C 3 HOH A 50 749 749 HOH HOH . C 3 HOH A 51 750 750 HOH HOH . C 3 HOH A 52 751 751 HOH HOH . C 3 HOH A 53 752 752 HOH HOH . C 3 HOH A 54 753 753 HOH HOH . C 3 HOH A 55 754 754 HOH HOH . C 3 HOH A 56 755 755 HOH HOH . C 3 HOH A 57 756 756 HOH HOH . C 3 HOH A 58 757 757 HOH HOH . C 3 HOH A 59 758 758 HOH HOH . C 3 HOH A 60 759 759 HOH HOH . C 3 HOH A 61 760 760 HOH HOH . C 3 HOH A 62 761 761 HOH HOH . C 3 HOH A 63 762 762 HOH HOH . C 3 HOH A 64 763 763 HOH HOH . C 3 HOH A 65 764 764 HOH HOH . C 3 HOH A 66 765 765 HOH HOH . C 3 HOH A 67 766 766 HOH HOH . C 3 HOH A 68 767 767 HOH HOH . C 3 HOH A 69 768 768 HOH HOH . C 3 HOH A 70 769 769 HOH HOH . C 3 HOH A 71 770 770 HOH HOH . C 3 HOH A 72 771 771 HOH HOH . C 3 HOH A 73 772 772 HOH HOH . C 3 HOH A 74 773 773 HOH HOH . C 3 HOH A 75 774 774 HOH HOH . C 3 HOH A 76 775 775 HOH HOH . C 3 HOH A 77 776 776 HOH HOH . C 3 HOH A 78 777 777 HOH HOH . C 3 HOH A 79 778 778 HOH HOH . C 3 HOH A 80 779 779 HOH HOH . C 3 HOH A 81 780 780 HOH HOH . C 3 HOH A 82 781 781 HOH HOH . C 3 HOH A 83 782 782 HOH HOH . C 3 HOH A 84 783 783 HOH HOH . C 3 HOH A 85 784 784 HOH HOH . C 3 HOH A 86 785 785 HOH HOH . C 3 HOH A 87 786 786 HOH HOH . C 3 HOH A 88 787 787 HOH HOH . C 3 HOH A 89 788 788 HOH HOH . C 3 HOH A 90 789 789 HOH HOH . C 3 HOH A 91 790 790 HOH HOH . C 3 HOH A 92 791 791 HOH HOH . C 3 HOH A 93 792 792 HOH HOH . C 3 HOH A 94 793 793 HOH HOH . C 3 HOH A 95 794 794 HOH HOH . C 3 HOH A 96 795 795 HOH HOH . C 3 HOH A 97 796 796 HOH HOH . C 3 HOH A 98 797 797 HOH HOH . C 3 HOH A 99 798 798 HOH HOH . C 3 HOH A 100 799 799 HOH HOH . C 3 HOH A 101 800 800 HOH HOH . C 3 HOH A 102 801 801 HOH HOH . C 3 HOH A 103 802 802 HOH HOH . C 3 HOH A 104 803 803 HOH HOH . C 3 HOH A 105 804 804 HOH HOH . C 3 HOH A 106 837 837 HOH HOH . C 3 HOH A 107 838 838 HOH HOH . C 3 HOH A 108 840 840 HOH HOH . C 3 HOH A 109 841 841 HOH HOH . C 3 HOH A 110 842 842 HOH HOH . C 3 HOH A 111 843 843 HOH HOH . C 3 HOH A 112 844 844 HOH HOH . C 3 HOH A 113 845 845 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 . . . B 2 -28.543 -9.078 20.224 1 62.36 ? N1 UMP 603 A 1 HETATM 2 C C2 UMP . . . B 2 -27.551 -8.077 20.209 1 61.11 ? C2 UMP 603 A 1 HETATM 3 N N3 UMP . . . B 2 -28.048 -6.781 20.029 1 62.61 ? N3 UMP 603 A 1 HETATM 4 C C4 UMP . . . B 2 -29.398 -6.42 19.869 1 61.78 ? C4 UMP 603 A 1 HETATM 5 C C5 UMP . . . B 2 -30.324 -7.538 19.881 1 63.16 ? C5 UMP 603 A 1 HETATM 6 C C6 UMP . . . B 2 -29.842 -8.837 20.062 1 63.09 ? C6 UMP 603 A 1 HETATM 7 O O2 UMP . . . B 2 -26.34 -8.278 20.319 1 55.49 ? O2 UMP 603 A 1 HETATM 8 O O4 UMP . . . B 2 -29.751 -5.241 19.778 1 61.38 ? O4 UMP 603 A 1 HETATM 9 C C1' UMP . . . B 2 -28.229 -10.496 20.496 1 61.88 ? C1' UMP 603 A 1 HETATM 10 C C2' UMP . . . B 2 -28 -10.789 21.98 1 59.05 ? C2' UMP 603 A 1 HETATM 11 C C3' UMP . . . B 2 -28.128 -12.303 22.028 1 58.67 ? C3' UMP 603 A 1 HETATM 12 C C4' UMP . . . B 2 -29.379 -12.645 21.202 1 59.68 ? C4' UMP 603 A 1 HETATM 13 O O3' UMP . . . B 2 -26.969 -12.855 21.36 1 51.81 ? O3' UMP 603 A 1 HETATM 14 O O4' UMP . . . B 2 -29.253 -11.57 20.141 1 62.44 ? O4' UMP 603 A 1 HETATM 15 C C5' UMP . . . B 2 -30.658 -12.399 22.016 1 57.95 ? C5' UMP 603 A 1 HETATM 16 O O5' UMP . . . B 2 -30.825 -13.43 23.06 1 53.95 ? O5' UMP 603 A 1 HETATM 17 P P UMP . . . B 2 -31.52 -13.273 24.48 1 46.58 ? P UMP 603 A 1 HETATM 18 O OP1 UMP . . . B 2 -30.72 -12.219 25.101 1 50.99 ? OP1 UMP 603 A 1 HETATM 19 O OP2 UMP . . . B 2 -32.97 -12.999 24.593 1 48.04 ? OP2 UMP 603 A 1 HETATM 20 O OP3 UMP . . . B 2 -31.289 -14.529 25.203 1 50.18 ? OP3 UMP 603 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #