data_5DEL # _model_server_result.job_id vDIuqS4U815bB1sviM421g _model_server_result.datetime_utc '2024-11-25 16:39:10' _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 5del # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5DEL # _exptl.entry_id 5DEL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 456.344 _entity.id 2 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 'FLAVIN MONONUCLEOTIDE' _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 120 _cell.entry_id 5DEL _cell.length_a 85.046 _cell.length_b 85.046 _cell.length_c 137.704 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DEL _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64' # _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,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 # _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 # _chem_comp.formula 'C17 H21 N4 O9 P' _chem_comp.formula_weight 456.344 _chem_comp.id FMN _chem_comp.mon_nstd_flag . _chem_comp.name 'FLAVIN MONONUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'RIBOFLAVIN MONOPHOSPHATE' # 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 FMN sing 115 n n N1 C10 FMN doub 116 n n C2 O2 FMN doub 117 n n C2 N3 FMN sing 118 n n N3 C4 FMN sing 119 n n N3 HN3 FMN sing 120 n n C4 O4 FMN doub 121 n n C4 C4A FMN sing 122 n n C4A N5 FMN doub 123 n n C4A C10 FMN sing 124 n n N5 C5A FMN sing 125 n n C5A C6 FMN doub 126 n y C5A C9A FMN sing 127 n y C6 C7 FMN sing 128 n y C6 H6 FMN sing 129 n n C7 C7M FMN sing 130 n n C7 C8 FMN doub 131 n y C7M HM71 FMN sing 132 n n C7M HM72 FMN sing 133 n n C7M HM73 FMN sing 134 n n C8 C8M FMN sing 135 n n C8 C9 FMN sing 136 n y C8M HM81 FMN sing 137 n n C8M HM82 FMN sing 138 n n C8M HM83 FMN sing 139 n n C9 C9A FMN doub 140 n y C9 H9 FMN sing 141 n n C9A N10 FMN sing 142 n n N10 C10 FMN sing 143 n n N10 C1' FMN sing 144 n n C1' C2' FMN sing 145 n n C1' "H1'1" FMN sing 146 n n C1' "H1'2" FMN sing 147 n n C2' O2' FMN sing 148 n n C2' C3' FMN sing 149 n n C2' H2' FMN sing 150 n n O2' HO2' FMN sing 151 n n C3' O3' FMN sing 152 n n C3' C4' FMN sing 153 n n C3' H3' FMN sing 154 n n O3' HO3' FMN sing 155 n n C4' O4' FMN sing 156 n n C4' C5' FMN sing 157 n n C4' H4' FMN sing 158 n n O4' HO4' FMN sing 159 n n C5' O5' FMN sing 160 n n C5' "H5'1" FMN sing 161 n n C5' "H5'2" FMN sing 162 n n O5' P FMN sing 163 n n P O1P FMN doub 164 n n P O2P FMN sing 165 n n P O3P FMN sing 166 n n O2P HOP2 FMN sing 167 n n O3P HOP3 FMN sing 168 n n # _atom_sites.entry_id 5DEL _atom_sites.fract_transf_matrix[1][1] 0.011758 _atom_sites.fract_transf_matrix[1][2] 0.006789 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013577 _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] 0.007262 _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 FMN A 1 601 1002 FMN FMN . C 3 ORO A 1 602 1003 ORO ORO . D 4 D59 A 1 603 1004 D59 D59 . E 5 GOL A 1 604 1005 GOL GOL . F 6 LDA A 1 605 1006 LDA LDA . G 5 GOL A 1 606 1007 GOL GOL . H 7 HOH A 1 701 154 HOH HOH . H 7 HOH A 2 702 164 HOH HOH . H 7 HOH A 3 703 90 HOH HOH . H 7 HOH A 4 704 74 HOH HOH . H 7 HOH A 5 705 48 HOH HOH . H 7 HOH A 6 706 19 HOH HOH . H 7 HOH A 7 707 60 HOH HOH . H 7 HOH A 8 708 61 HOH HOH . H 7 HOH A 9 709 85 HOH HOH . H 7 HOH A 10 710 9 HOH HOH . H 7 HOH A 11 711 54 HOH HOH . H 7 HOH A 12 712 141 HOH HOH . H 7 HOH A 13 713 137 HOH HOH . H 7 HOH A 14 714 15 HOH HOH . H 7 HOH A 15 715 37 HOH HOH . H 7 HOH A 16 716 94 HOH HOH . H 7 HOH A 17 717 130 HOH HOH . H 7 HOH A 18 718 73 HOH HOH . H 7 HOH A 19 719 72 HOH HOH . H 7 HOH A 20 720 11 HOH HOH . H 7 HOH A 21 721 62 HOH HOH . H 7 HOH A 22 722 31 HOH HOH . H 7 HOH A 23 723 12 HOH HOH . H 7 HOH A 24 724 126 HOH HOH . H 7 HOH A 25 725 41 HOH HOH . H 7 HOH A 26 726 69 HOH HOH . H 7 HOH A 27 727 63 HOH HOH . H 7 HOH A 28 728 17 HOH HOH . H 7 HOH A 29 729 171 HOH HOH . H 7 HOH A 30 730 151 HOH HOH . H 7 HOH A 31 731 14 HOH HOH . H 7 HOH A 32 732 25 HOH HOH . H 7 HOH A 33 733 10 HOH HOH . H 7 HOH A 34 734 47 HOH HOH . H 7 HOH A 35 735 93 HOH HOH . H 7 HOH A 36 736 39 HOH HOH . H 7 HOH A 37 737 5 HOH HOH . H 7 HOH A 38 738 89 HOH HOH . H 7 HOH A 39 739 78 HOH HOH . H 7 HOH A 40 740 179 HOH HOH . H 7 HOH A 41 741 33 HOH HOH . H 7 HOH A 42 742 6 HOH HOH . H 7 HOH A 43 743 142 HOH HOH . H 7 HOH A 44 744 20 HOH HOH . H 7 HOH A 45 745 108 HOH HOH . H 7 HOH A 46 746 36 HOH HOH . H 7 HOH A 47 747 40 HOH HOH . H 7 HOH A 48 748 30 HOH HOH . H 7 HOH A 49 749 32 HOH HOH . H 7 HOH A 50 750 8 HOH HOH . H 7 HOH A 51 751 49 HOH HOH . H 7 HOH A 52 752 42 HOH HOH . H 7 HOH A 53 753 105 HOH HOH . H 7 HOH A 54 754 116 HOH HOH . H 7 HOH A 55 755 57 HOH HOH . H 7 HOH A 56 756 2 HOH HOH . H 7 HOH A 57 757 1 HOH HOH . H 7 HOH A 58 758 16 HOH HOH . H 7 HOH A 59 759 86 HOH HOH . H 7 HOH A 60 760 26 HOH HOH . H 7 HOH A 61 761 27 HOH HOH . H 7 HOH A 62 762 3 HOH HOH . H 7 HOH A 63 763 82 HOH HOH . H 7 HOH A 64 764 76 HOH HOH . H 7 HOH A 65 765 75 HOH HOH . H 7 HOH A 66 766 101 HOH HOH . H 7 HOH A 67 767 103 HOH HOH . H 7 HOH A 68 768 77 HOH HOH . H 7 HOH A 69 769 95 HOH HOH . H 7 HOH A 70 770 112 HOH HOH . H 7 HOH A 71 771 160 HOH HOH . H 7 HOH A 72 772 34 HOH HOH . H 7 HOH A 73 773 13 HOH HOH . H 7 HOH A 74 774 188 HOH HOH . H 7 HOH A 75 775 87 HOH HOH . H 7 HOH A 76 776 139 HOH HOH . H 7 HOH A 77 777 51 HOH HOH . H 7 HOH A 78 778 56 HOH HOH . H 7 HOH A 79 779 43 HOH HOH . H 7 HOH A 80 780 187 HOH HOH . H 7 HOH A 81 781 177 HOH HOH . H 7 HOH A 82 782 46 HOH HOH . H 7 HOH A 83 783 55 HOH HOH . H 7 HOH A 84 784 91 HOH HOH . H 7 HOH A 85 785 38 HOH HOH . H 7 HOH A 86 786 110 HOH HOH . H 7 HOH A 87 787 80 HOH HOH . H 7 HOH A 88 788 166 HOH HOH . H 7 HOH A 89 789 44 HOH HOH . H 7 HOH A 90 790 64 HOH HOH . H 7 HOH A 91 791 152 HOH HOH . H 7 HOH A 92 792 109 HOH HOH . H 7 HOH A 93 793 132 HOH HOH . H 7 HOH A 94 794 92 HOH HOH . H 7 HOH A 95 795 67 HOH HOH . H 7 HOH A 96 796 190 HOH HOH . H 7 HOH A 97 797 22 HOH HOH . H 7 HOH A 98 798 99 HOH HOH . H 7 HOH A 99 799 88 HOH HOH . H 7 HOH A 100 800 131 HOH HOH . H 7 HOH A 101 801 24 HOH HOH . H 7 HOH A 102 802 45 HOH HOH . H 7 HOH A 103 803 96 HOH HOH . H 7 HOH A 104 804 150 HOH HOH . H 7 HOH A 105 805 136 HOH HOH . H 7 HOH A 106 806 168 HOH HOH . H 7 HOH A 107 807 58 HOH HOH . H 7 HOH A 108 808 65 HOH HOH . H 7 HOH A 109 809 79 HOH HOH . H 7 HOH A 110 810 70 HOH HOH . H 7 HOH A 111 811 123 HOH HOH . H 7 HOH A 112 812 107 HOH HOH . H 7 HOH A 113 813 176 HOH HOH . H 7 HOH A 114 814 135 HOH HOH . H 7 HOH A 115 815 106 HOH HOH . H 7 HOH A 116 816 165 HOH HOH . H 7 HOH A 117 817 113 HOH HOH . H 7 HOH A 118 818 125 HOH HOH . H 7 HOH A 119 819 52 HOH HOH . H 7 HOH A 120 820 50 HOH HOH . H 7 HOH A 121 821 155 HOH HOH . H 7 HOH A 122 822 163 HOH HOH . H 7 HOH A 123 823 145 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 FMN . . . B 2 -3.33 21.3 -2.43 1 9.65 ? N1 FMN 601 A 1 HETATM 2 C C2 FMN . . . B 2 -2.797 20.305 -1.637 1 11.71 ? C2 FMN 601 A 1 HETATM 3 O O2 FMN . . . B 2 -3.048 20.28 -0.431 1 16.03 ? O2 FMN 601 A 1 HETATM 4 N N3 FMN . . . B 2 -1.985 19.342 -2.193 1 9.88 ? N3 FMN 601 A 1 HETATM 5 C C4 FMN . . . B 2 -1.707 19.373 -3.542 1 8.21 ? C4 FMN 601 A 1 HETATM 6 O O4 FMN . . . B 2 -0.975 18.512 -4.045 1 3.89 ? O4 FMN 601 A 1 HETATM 7 C C4A FMN . . . B 2 -2.243 20.372 -4.34 1 10.49 ? C4A FMN 601 A 1 HETATM 8 N N5 FMN . . . B 2 -1.968 20.397 -5.692 1 10.48 ? N5 FMN 601 A 1 HETATM 9 C C5A FMN . . . B 2 -2.49 21.396 -6.482 1 11.38 ? C5A FMN 601 A 1 HETATM 10 C C6 FMN . . . B 2 -2.194 21.412 -7.837 1 12.26 ? C6 FMN 601 A 1 HETATM 11 C C7 FMN . . . B 2 -2.711 22.405 -8.66 1 12.28 ? C7 FMN 601 A 1 HETATM 12 C C7M FMN . . . B 2 -2.358 22.37 -10.126 1 12.05 ? C7M FMN 601 A 1 HETATM 13 C C8 FMN . . . B 2 -3.536 23.384 -8.111 1 13.7 ? C8 FMN 601 A 1 HETATM 14 C C8M FMN . . . B 2 -4.117 24.478 -8.959 1 17.07 ? C8M FMN 601 A 1 HETATM 15 C C9 FMN . . . B 2 -3.827 23.365 -6.753 1 13.04 ? C9 FMN 601 A 1 HETATM 16 C C9A FMN . . . B 2 -3.308 22.372 -5.925 1 12.58 ? C9A FMN 601 A 1 HETATM 17 N N10 FMN . . . B 2 -3.597 22.343 -4.567 1 13.6 ? N10 FMN 601 A 1 HETATM 18 C C10 FMN . . . B 2 -3.059 21.344 -3.78 1 11.24 ? C10 FMN 601 A 1 HETATM 19 C C1' FMN . . . B 2 -4.477 23.389 -3.93 1 15.07 ? C1' FMN 601 A 1 HETATM 20 C C2' FMN . . . B 2 -3.63 24.609 -3.579 1 12.86 ? C2' FMN 601 A 1 HETATM 21 O O2' FMN . . . B 2 -2.658 24.2 -2.644 1 10.36 ? O2' FMN 601 A 1 HETATM 22 C C3' FMN . . . B 2 -4.425 25.749 -2.955 1 14.02 ? C3' FMN 601 A 1 HETATM 23 O O3' FMN . . . B 2 -4.914 25.327 -1.703 1 18.89 ? O3' FMN 601 A 1 HETATM 24 C C4' FMN . . . B 2 -5.577 26.18 -3.853 1 14.57 ? C4' FMN 601 A 1 HETATM 25 O O4' FMN . . . B 2 -5.111 26.313 -5.182 1 18.37 ? O4' FMN 601 A 1 HETATM 26 C C5' FMN . . . B 2 -6.206 27.501 -3.424 1 14.08 ? C5' FMN 601 A 1 HETATM 27 O O5' FMN . . . B 2 -5.222 28.513 -3.416 1 15.13 ? O5' FMN 601 A 1 HETATM 28 P P FMN . . . B 2 -5.218 29.7 -4.504 1 22.82 ? P FMN 601 A 1 HETATM 29 O O1P FMN . . . B 2 -4.68 29.141 -5.796 1 18.55 ? O1P FMN 601 A 1 HETATM 30 O O2P FMN . . . B 2 -4.323 30.821 -4.021 1 28.08 ? O2P FMN 601 A 1 HETATM 31 O O3P FMN . . . B 2 -6.626 30.204 -4.724 1 21.46 ? O3P FMN 601 A 1 HETATM 32 H HN3 FMN . . . B 2 -1.546 18.62 -1.587 1 11.86 ? HN3 FMN 601 A 1 HETATM 33 H H6 FMN . . . B 2 -1.552 20.64 -8.259 1 14.72 ? H6 FMN 601 A 1 HETATM 34 H HM71 FMN . . . B 2 -2.84 23.204 -10.636 1 14.46 ? HM71 FMN 601 A 1 HETATM 35 H HM72 FMN . . . B 2 -2.7 21.431 -10.56 1 14.46 ? HM72 FMN 601 A 1 HETATM 36 H HM73 FMN . . . B 2 -1.277 22.45 -10.241 1 14.46 ? HM73 FMN 601 A 1 HETATM 37 H HM81 FMN . . . B 2 -4.722 25.137 -8.336 1 20.49 ? HM81 FMN 601 A 1 HETATM 38 H HM82 FMN . . . B 2 -4.742 24.041 -9.738 1 20.49 ? HM82 FMN 601 A 1 HETATM 39 H HM83 FMN . . . B 2 -3.311 25.05 -9.417 1 20.49 ? HM83 FMN 601 A 1 HETATM 40 H H9 FMN . . . B 2 -4.47 24.137 -6.33 1 15.65 ? H9 FMN 601 A 1 HETATM 41 H "H1'1" FMN . . . B 2 -5.27 23.675 -4.621 1 18.09 ? "H1'1" FMN 601 A 1 HETATM 42 H "H1'2" FMN . . . B 2 -4.938 22.986 -3.028 1 18.09 ? "H1'2" FMN 601 A 1 HETATM 43 H H2' FMN . . . B 2 -3.145 24.973 -4.485 1 15.44 ? H2' FMN 601 A 1 HETATM 44 H HO2' FMN . . . B 2 -2.735 24.746 -1.834 1 12.44 ? HO2' FMN 601 A 1 HETATM 45 H H3' FMN . . . B 2 -3.758 26.6 -2.818 1 16.83 ? H3' FMN 601 A 1 HETATM 46 H H4' FMN . . . B 2 -6.346 25.409 -3.816 1 17.49 ? H4' FMN 601 A 1 HETATM 47 H HO4' FMN . . . B 2 -5.303 27.217 -5.507 1 22.05 ? HO4' FMN 601 A 1 HETATM 48 H "H5'1" FMN . . . B 2 -7.006 27.77 -4.114 1 16.9 ? "H5'1" FMN 601 A 1 HETATM 49 H "H5'2" FMN . . . B 2 -6.636 27.397 -2.428 1 16.9 ? "H5'2" FMN 601 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 49 #