data_4ZQM # _model_server_result.job_id zzxiOnjfHwp9RpWR_kMaJg _model_server_result.datetime_utc '2024-11-26 08:50:48' _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 4zqm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 4ZQM # _exptl.entry_id 4ZQM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 365.213 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "XANTHOSINE-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 4ZQM _cell.length_a 88.154 _cell.length_b 88.154 _cell.length_c 85.512 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZQM _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 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 'C10 H14 N4 O9 P 1' _chem_comp.formula_weight 365.213 _chem_comp.id XMP _chem_comp.mon_nstd_flag . _chem_comp.name "XANTHOSINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE' # 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 P O1P XMP sing 451 n n P O2P XMP sing 452 n n P O5' XMP sing 453 n n P O3P XMP doub 454 n n O1P HOP1 XMP sing 455 n n O2P HOP2 XMP sing 456 n n O5' C5' XMP sing 457 n n C5' C4' XMP sing 458 n n C5' "H5'2" XMP sing 459 n n C5' "H5'1" XMP sing 460 n n C4' O4' XMP sing 461 n n C4' C3' XMP sing 462 n n C4' H4' XMP sing 463 n n O4' C1' XMP sing 464 n n C1' N9 XMP sing 465 n n C1' C2' XMP sing 466 n n C1' H1' XMP sing 467 n n N9 C4 XMP sing 468 n y N9 C8 XMP sing 469 n y C4 N3 XMP sing 470 n n C4 C5 XMP doub 471 n y N3 C2 XMP sing 472 n n N3 H3 XMP sing 473 n n N1 C2 XMP sing 474 n n N1 C6 XMP sing 475 n n N1 H1 XMP sing 476 n n C2 O2 XMP doub 477 n n C6 O6 XMP doub 478 n n C6 C5 XMP sing 479 n n C5 N7 XMP sing 480 n y N7 C8 XMP doub 481 n y N7 H7 XMP sing 482 n n C8 H8 XMP sing 483 n n C2' O2' XMP sing 484 n n C2' C3' XMP sing 485 n n C2' H2' XMP sing 486 n n O2' H2O1 XMP sing 487 n n C3' O3' XMP sing 488 n n C3' H3' XMP sing 489 n n O3' H3O1 XMP sing 490 n n # _atom_sites.entry_id 4ZQM _atom_sites.fract_transf_matrix[1][1] 0.011344 _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] 0.011344 _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] 0.011694 _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 XMP A 1 601 550 XMP XMP . C 3 NAD A 1 602 551 NAD NAD . D 4 HOH A 1 701 100 HOH HOH . D 4 HOH A 2 702 114 HOH HOH . D 4 HOH A 3 703 139 HOH HOH . D 4 HOH A 4 704 157 HOH HOH . D 4 HOH A 5 705 115 HOH HOH . D 4 HOH A 6 706 147 HOH HOH . D 4 HOH A 7 707 143 HOH HOH . D 4 HOH A 8 708 49 HOH HOH . D 4 HOH A 9 709 113 HOH HOH . D 4 HOH A 10 710 92 HOH HOH . D 4 HOH A 11 711 66 HOH HOH . D 4 HOH A 12 712 145 HOH HOH . D 4 HOH A 13 713 27 HOH HOH . D 4 HOH A 14 714 110 HOH HOH . D 4 HOH A 15 715 134 HOH HOH . D 4 HOH A 16 716 70 HOH HOH . D 4 HOH A 17 717 133 HOH HOH . D 4 HOH A 18 718 119 HOH HOH . D 4 HOH A 19 719 94 HOH HOH . D 4 HOH A 20 720 101 HOH HOH . D 4 HOH A 21 721 41 HOH HOH . D 4 HOH A 22 722 106 HOH HOH . D 4 HOH A 23 723 65 HOH HOH . D 4 HOH A 24 724 131 HOH HOH . D 4 HOH A 25 725 21 HOH HOH . D 4 HOH A 26 726 75 HOH HOH . D 4 HOH A 27 727 80 HOH HOH . D 4 HOH A 28 728 56 HOH HOH . D 4 HOH A 29 729 84 HOH HOH . D 4 HOH A 30 730 88 HOH HOH . D 4 HOH A 31 731 154 HOH HOH . D 4 HOH A 32 732 81 HOH HOH . D 4 HOH A 33 733 73 HOH HOH . D 4 HOH A 34 734 3 HOH HOH . D 4 HOH A 35 735 159 HOH HOH . D 4 HOH A 36 736 135 HOH HOH . D 4 HOH A 37 737 108 HOH HOH . D 4 HOH A 38 738 76 HOH HOH . D 4 HOH A 39 739 117 HOH HOH . D 4 HOH A 40 740 42 HOH HOH . D 4 HOH A 41 741 32 HOH HOH . D 4 HOH A 42 742 18 HOH HOH . D 4 HOH A 43 743 54 HOH HOH . D 4 HOH A 44 744 60 HOH HOH . D 4 HOH A 45 745 48 HOH HOH . D 4 HOH A 46 746 12 HOH HOH . D 4 HOH A 47 747 107 HOH HOH . D 4 HOH A 48 748 25 HOH HOH . D 4 HOH A 49 749 11 HOH HOH . D 4 HOH A 50 750 14 HOH HOH . D 4 HOH A 51 751 148 HOH HOH . D 4 HOH A 52 752 97 HOH HOH . D 4 HOH A 53 753 129 HOH HOH . D 4 HOH A 54 754 112 HOH HOH . D 4 HOH A 55 755 8 HOH HOH . D 4 HOH A 56 756 58 HOH HOH . D 4 HOH A 57 757 1 HOH HOH . D 4 HOH A 58 758 39 HOH HOH . D 4 HOH A 59 759 69 HOH HOH . D 4 HOH A 60 760 5 HOH HOH . D 4 HOH A 61 761 29 HOH HOH . D 4 HOH A 62 762 15 HOH HOH . D 4 HOH A 63 763 138 HOH HOH . D 4 HOH A 64 764 13 HOH HOH . D 4 HOH A 65 765 9 HOH HOH . D 4 HOH A 66 766 68 HOH HOH . D 4 HOH A 67 767 47 HOH HOH . D 4 HOH A 68 768 64 HOH HOH . D 4 HOH A 69 769 104 HOH HOH . D 4 HOH A 70 770 102 HOH HOH . D 4 HOH A 71 771 22 HOH HOH . D 4 HOH A 72 772 24 HOH HOH . D 4 HOH A 73 773 96 HOH HOH . D 4 HOH A 74 774 10 HOH HOH . D 4 HOH A 75 775 74 HOH HOH . D 4 HOH A 76 776 46 HOH HOH . D 4 HOH A 77 777 78 HOH HOH . D 4 HOH A 78 778 116 HOH HOH . D 4 HOH A 79 779 33 HOH HOH . D 4 HOH A 80 780 23 HOH HOH . D 4 HOH A 81 781 128 HOH HOH . D 4 HOH A 82 782 130 HOH HOH . D 4 HOH A 83 783 55 HOH HOH . D 4 HOH A 84 784 98 HOH HOH . D 4 HOH A 85 785 99 HOH HOH . D 4 HOH A 86 786 28 HOH HOH . D 4 HOH A 87 787 19 HOH HOH . D 4 HOH A 88 788 125 HOH HOH . D 4 HOH A 89 789 109 HOH HOH . D 4 HOH A 90 790 72 HOH HOH . D 4 HOH A 91 791 17 HOH HOH . D 4 HOH A 92 792 44 HOH HOH . D 4 HOH A 93 793 118 HOH HOH . D 4 HOH A 94 794 50 HOH HOH . D 4 HOH A 95 795 34 HOH HOH . D 4 HOH A 96 796 95 HOH HOH . D 4 HOH A 97 797 20 HOH HOH . D 4 HOH A 98 798 71 HOH HOH . D 4 HOH A 99 799 121 HOH HOH . D 4 HOH A 100 800 111 HOH HOH . D 4 HOH A 101 801 126 HOH HOH . D 4 HOH A 102 802 105 HOH HOH . D 4 HOH A 103 803 63 HOH HOH . D 4 HOH A 104 804 140 HOH HOH . D 4 HOH A 105 805 51 HOH HOH . D 4 HOH A 106 806 160 HOH HOH . D 4 HOH A 107 807 124 HOH HOH . D 4 HOH A 108 808 16 HOH HOH . D 4 HOH A 109 809 37 HOH HOH . D 4 HOH A 110 810 82 HOH HOH . D 4 HOH A 111 811 43 HOH HOH . D 4 HOH A 112 812 86 HOH HOH . D 4 HOH A 113 813 123 HOH HOH . D 4 HOH A 114 814 146 HOH HOH . D 4 HOH A 115 815 153 HOH HOH . D 4 HOH A 116 816 62 HOH HOH . D 4 HOH A 117 817 7 HOH HOH . D 4 HOH A 118 818 79 HOH HOH . D 4 HOH A 119 819 30 HOH HOH . D 4 HOH A 120 820 6 HOH HOH . D 4 HOH A 121 821 103 HOH HOH . D 4 HOH A 122 822 26 HOH HOH . D 4 HOH A 123 823 53 HOH HOH . D 4 HOH A 124 824 137 HOH HOH . D 4 HOH A 125 825 52 HOH HOH . D 4 HOH A 126 826 36 HOH HOH . D 4 HOH A 127 827 93 HOH HOH . D 4 HOH A 128 828 35 HOH HOH . D 4 HOH A 129 829 57 HOH HOH . D 4 HOH A 130 830 152 HOH HOH . D 4 HOH A 131 831 67 HOH HOH . D 4 HOH A 132 832 4 HOH HOH . D 4 HOH A 133 833 150 HOH HOH . D 4 HOH A 134 834 31 HOH HOH . D 4 HOH A 135 835 38 HOH HOH . D 4 HOH A 136 836 142 HOH HOH . D 4 HOH A 137 837 2 HOH HOH . D 4 HOH A 138 838 120 HOH HOH . D 4 HOH A 139 839 40 HOH HOH . D 4 HOH A 140 840 144 HOH HOH . D 4 HOH A 141 841 151 HOH HOH . D 4 HOH A 142 842 132 HOH HOH . D 4 HOH A 143 843 161 HOH HOH . D 4 HOH A 144 844 141 HOH HOH . D 4 HOH A 145 845 91 HOH HOH . D 4 HOH A 146 846 156 HOH HOH . D 4 HOH A 147 847 85 HOH HOH . D 4 HOH A 148 848 89 HOH HOH . D 4 HOH A 149 849 59 HOH HOH . D 4 HOH A 150 850 158 HOH HOH . D 4 HOH A 151 851 155 HOH HOH . D 4 HOH A 152 852 149 HOH HOH . D 4 HOH A 153 853 127 HOH HOH . D 4 HOH A 154 854 45 HOH HOH . D 4 HOH A 155 855 87 HOH HOH . D 4 HOH A 156 856 61 HOH HOH . D 4 HOH A 157 857 90 HOH HOH . D 4 HOH A 158 858 83 HOH HOH . D 4 HOH A 159 859 122 HOH HOH . D 4 HOH A 160 860 77 HOH HOH . D 4 HOH A 161 861 136 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 P P XMP . . . B 2 -19.394 11.356 5.621 1 20.15 ? P XMP 601 A 1 HETATM 2 O O1P XMP . . . B 2 -19.431 12.835 5.337 1 21.18 ? O1P XMP 601 A 1 HETATM 3 O O2P XMP . . . B 2 -19.587 11.023 7.08 1 24.44 ? O2P XMP 601 A 1 HETATM 4 O O5' XMP . . . B 2 -20.597 10.758 4.77 1 20.73 ? O5' XMP 601 A 1 HETATM 5 O O3P XMP . . . B 2 -18.162 10.676 5.058 1 19.32 ? O3P XMP 601 A 1 HETATM 6 C C5' XMP . . . B 2 -21.942 11.149 4.983 1 20.93 ? C5' XMP 601 A 1 HETATM 7 C C4' XMP . . . B 2 -22.825 10.513 3.936 1 19.71 ? C4' XMP 601 A 1 HETATM 8 O O4' XMP . . . B 2 -22.923 9.09 4.175 1 22.36 ? O4' XMP 601 A 1 HETATM 9 C C1' XMP . . . B 2 -24.154 8.608 3.643 1 20.49 ? C1' XMP 601 A 1 HETATM 10 N N9 XMP . . . B 2 -24.831 7.802 4.668 1 22.23 ? N9 XMP 601 A 1 HETATM 11 C C4 XMP . . . B 2 -24.685 6.494 4.687 1 24.95 ? C4 XMP 601 A 1 HETATM 12 N N3 XMP . . . B 2 -24.055 5.628 3.894 1 25.38 ? N3 XMP 601 A 1 HETATM 13 N N1 XMP . . . B 2 -24.744 3.818 5.251 1 27.12 ? N1 XMP 601 A 1 HETATM 14 C C2 XMP . . . B 2 -24.117 4.314 4.169 1 31.63 ? C2 XMP 601 A 1 HETATM 15 O O2 XMP . . . B 2 -23.544 3.515 3.397 1 35.75 ? O2 XMP 601 A 1 HETATM 16 C C6 XMP . . . B 2 -25.409 4.6 6.115 1 26.84 ? C6 XMP 601 A 1 HETATM 17 O O6 XMP . . . B 2 -26.003 4.139 7.11 1 26.51 ? O6 XMP 601 A 1 HETATM 18 C C5 XMP . . . B 2 -25.409 6.041 5.87 1 21.41 ? C5 XMP 601 A 1 HETATM 19 N N7 XMP . . . B 2 -25.908 7.126 6.472 1 22.41 ? N7 XMP 601 A 1 HETATM 20 C C8 XMP . . . B 2 -25.55 8.207 5.737 1 23.56 ? C8 XMP 601 A 1 HETATM 21 C C2' XMP . . . B 2 -24.967 9.809 3.181 1 20.35 ? C2' XMP 601 A 1 HETATM 22 O O2' XMP . . . B 2 -24.801 9.907 1.765 1 22.08 ? O2' XMP 601 A 1 HETATM 23 C C3' XMP . . . B 2 -24.272 10.953 3.928 1 19 ? C3' XMP 601 A 1 HETATM 24 O O3' XMP . . . B 2 -24.466 12.231 3.368 1 19.19 ? O3' XMP 601 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #