data_4QQ3 # _model_server_result.job_id CCQY4TDuphwDjM6wfJKzGQ _model_server_result.datetime_utc '2024-11-26 16:15:36' _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 4qq3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4QQ3 # _exptl.entry_id 4QQ3 _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 4QQ3 _cell.length_a 106.9 _cell.length_b 106.9 _cell.length_c 65.489 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QQ3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 21 2' # _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,E _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_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 106.9 0 3 'crystal symmetry operation' 3_555 -y+1/2,x+1/2,z 0 -1 0 1 0 0 0 0 1 53.45 53.45 0 4 'crystal symmetry operation' 4_455 y-1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 -53.45 53.45 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 348 n n P O2P XMP sing 349 n n P O5' XMP sing 350 n n P O3P XMP doub 351 n n O1P HOP1 XMP sing 352 n n O2P HOP2 XMP sing 353 n n O5' C5' XMP sing 354 n n C5' C4' XMP sing 355 n n C5' "H5'2" XMP sing 356 n n C5' "H5'1" XMP sing 357 n n C4' O4' XMP sing 358 n n C4' C3' XMP sing 359 n n C4' H4' XMP sing 360 n n O4' C1' XMP sing 361 n n C1' N9 XMP sing 362 n n C1' C2' XMP sing 363 n n C1' H1' XMP sing 364 n n N9 C4 XMP sing 365 n y N9 C8 XMP sing 366 n y C4 N3 XMP sing 367 n n C4 C5 XMP doub 368 n y N3 C2 XMP sing 369 n n N3 H3 XMP sing 370 n n N1 C2 XMP sing 371 n n N1 C6 XMP sing 372 n n N1 H1 XMP sing 373 n n C2 O2 XMP doub 374 n n C6 O6 XMP doub 375 n n C6 C5 XMP sing 376 n n C5 N7 XMP sing 377 n y N7 C8 XMP doub 378 n y N7 H7 XMP sing 379 n n C8 H8 XMP sing 380 n n C2' O2' XMP sing 381 n n C2' C3' XMP sing 382 n n C2' H2' XMP sing 383 n n O2' H2O1 XMP sing 384 n n C3' O3' XMP sing 385 n n C3' H3' XMP sing 386 n n O3' H3O1 XMP sing 387 n n # _atom_sites.entry_id 4QQ3 _atom_sites.fract_transf_matrix[1][1] 0.009355 _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] 0.009355 _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] 0.01527 _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 1 501 501 XMP XMP . C 3 CL A 1 502 502 CL CL . D 3 CL A 1 503 503 CL CL . E 4 HOH A 1 601 1 HOH HOH . E 4 HOH A 2 602 2 HOH HOH . E 4 HOH A 3 603 3 HOH HOH . E 4 HOH A 4 604 4 HOH HOH . E 4 HOH A 5 605 5 HOH HOH . E 4 HOH A 6 606 6 HOH HOH . E 4 HOH A 7 607 7 HOH HOH . E 4 HOH A 8 608 8 HOH HOH . E 4 HOH A 9 609 9 HOH HOH . E 4 HOH A 10 610 10 HOH HOH . E 4 HOH A 11 611 11 HOH HOH . E 4 HOH A 12 612 12 HOH HOH . E 4 HOH A 13 613 13 HOH HOH . E 4 HOH A 14 614 14 HOH HOH . E 4 HOH A 15 615 15 HOH HOH . E 4 HOH A 16 616 16 HOH HOH . E 4 HOH A 17 617 17 HOH HOH . E 4 HOH A 18 618 18 HOH HOH . E 4 HOH A 19 619 19 HOH HOH . E 4 HOH A 20 620 20 HOH HOH . E 4 HOH A 21 621 21 HOH HOH . E 4 HOH A 22 622 22 HOH HOH . E 4 HOH A 23 623 23 HOH HOH . E 4 HOH A 24 624 24 HOH HOH . E 4 HOH A 25 625 25 HOH HOH . E 4 HOH A 26 626 26 HOH HOH . E 4 HOH A 27 627 27 HOH HOH . E 4 HOH A 28 628 28 HOH HOH . E 4 HOH A 29 629 29 HOH HOH . E 4 HOH A 30 630 30 HOH HOH . E 4 HOH A 31 631 31 HOH HOH . E 4 HOH A 32 632 32 HOH HOH . E 4 HOH A 33 633 33 HOH HOH . E 4 HOH A 34 634 34 HOH HOH . E 4 HOH A 35 635 35 HOH HOH . E 4 HOH A 36 636 36 HOH HOH . E 4 HOH A 37 637 37 HOH HOH . E 4 HOH A 38 638 38 HOH HOH . E 4 HOH A 39 639 39 HOH HOH . E 4 HOH A 40 640 40 HOH HOH . E 4 HOH A 41 641 41 HOH HOH . E 4 HOH A 42 642 42 HOH HOH . E 4 HOH A 43 643 43 HOH HOH . E 4 HOH A 44 644 44 HOH HOH . E 4 HOH A 45 645 45 HOH HOH . E 4 HOH A 46 646 46 HOH HOH . E 4 HOH A 47 647 47 HOH HOH . E 4 HOH A 48 648 48 HOH HOH . E 4 HOH A 49 649 49 HOH HOH . E 4 HOH A 50 650 50 HOH HOH . E 4 HOH A 51 651 51 HOH HOH . E 4 HOH A 52 652 52 HOH HOH . E 4 HOH A 53 653 53 HOH HOH . E 4 HOH A 54 654 54 HOH HOH . E 4 HOH A 55 655 55 HOH HOH . E 4 HOH A 56 656 56 HOH HOH . E 4 HOH A 57 657 57 HOH HOH . E 4 HOH A 58 658 58 HOH HOH . E 4 HOH A 59 659 59 HOH HOH . E 4 HOH A 60 660 60 HOH HOH . E 4 HOH A 61 661 61 HOH HOH . E 4 HOH A 62 662 62 HOH HOH . E 4 HOH A 63 663 63 HOH HOH . E 4 HOH A 64 664 64 HOH HOH . E 4 HOH A 65 665 65 HOH HOH . E 4 HOH A 66 666 66 HOH HOH . E 4 HOH A 67 667 67 HOH HOH . E 4 HOH A 68 668 68 HOH HOH . E 4 HOH A 69 669 69 HOH HOH . E 4 HOH A 70 670 70 HOH HOH . E 4 HOH A 71 671 71 HOH HOH . E 4 HOH A 72 672 72 HOH HOH . E 4 HOH A 73 673 73 HOH HOH . E 4 HOH A 74 674 74 HOH HOH . E 4 HOH A 75 675 75 HOH HOH . E 4 HOH A 76 676 76 HOH HOH . E 4 HOH A 77 677 77 HOH HOH . E 4 HOH A 78 678 78 HOH HOH . E 4 HOH A 79 679 79 HOH HOH . E 4 HOH A 80 680 80 HOH HOH . E 4 HOH A 81 681 81 HOH HOH . E 4 HOH A 82 682 82 HOH HOH . E 4 HOH A 83 683 83 HOH HOH . E 4 HOH A 84 684 84 HOH HOH . E 4 HOH A 85 685 85 HOH HOH . E 4 HOH A 86 686 86 HOH HOH . E 4 HOH A 87 687 87 HOH HOH . E 4 HOH A 88 688 88 HOH HOH . E 4 HOH A 89 689 89 HOH HOH . E 4 HOH A 90 690 90 HOH HOH . E 4 HOH A 91 691 91 HOH HOH . E 4 HOH A 92 692 92 HOH HOH . E 4 HOH A 93 693 93 HOH HOH . E 4 HOH A 94 694 94 HOH HOH . E 4 HOH A 95 695 95 HOH HOH . E 4 HOH A 96 696 96 HOH HOH . E 4 HOH A 97 697 97 HOH HOH . E 4 HOH A 98 698 98 HOH HOH . E 4 HOH A 99 699 99 HOH HOH . E 4 HOH A 100 700 100 HOH HOH . E 4 HOH A 101 701 101 HOH HOH . E 4 HOH A 102 702 102 HOH HOH . E 4 HOH A 103 703 103 HOH HOH . E 4 HOH A 104 704 104 HOH HOH . E 4 HOH A 105 705 105 HOH HOH . E 4 HOH A 106 706 106 HOH HOH . E 4 HOH A 107 707 107 HOH HOH . E 4 HOH A 108 708 108 HOH HOH . E 4 HOH A 109 709 109 HOH HOH . E 4 HOH A 110 710 110 HOH HOH . E 4 HOH A 111 711 111 HOH HOH . E 4 HOH A 112 712 112 HOH HOH . E 4 HOH A 113 713 113 HOH HOH . E 4 HOH A 114 714 114 HOH HOH . E 4 HOH A 115 715 115 HOH HOH . E 4 HOH A 116 716 116 HOH HOH . E 4 HOH A 117 717 117 HOH HOH . E 4 HOH A 118 718 118 HOH HOH . E 4 HOH A 119 719 119 HOH HOH . E 4 HOH A 120 720 120 HOH HOH . E 4 HOH A 121 721 121 HOH HOH . E 4 HOH A 122 722 122 HOH HOH . E 4 HOH A 123 723 123 HOH HOH . E 4 HOH A 124 724 124 HOH HOH . E 4 HOH A 125 725 125 HOH HOH . E 4 HOH A 126 726 126 HOH HOH . E 4 HOH A 127 727 127 HOH HOH . E 4 HOH A 128 728 128 HOH HOH . E 4 HOH A 129 729 129 HOH HOH . E 4 HOH A 130 730 130 HOH HOH . E 4 HOH A 131 731 131 HOH HOH . E 4 HOH A 132 732 132 HOH HOH . E 4 HOH A 133 733 133 HOH HOH . E 4 HOH A 134 734 134 HOH HOH . E 4 HOH A 135 735 135 HOH HOH . E 4 HOH A 136 736 136 HOH HOH . E 4 HOH A 137 737 137 HOH HOH . E 4 HOH A 138 738 138 HOH HOH . E 4 HOH A 139 739 139 HOH HOH . E 4 HOH A 140 740 140 HOH HOH . E 4 HOH A 141 741 141 HOH HOH . E 4 HOH A 142 742 142 HOH HOH . E 4 HOH A 143 743 143 HOH HOH . E 4 HOH A 144 744 144 HOH HOH . E 4 HOH A 145 745 145 HOH HOH . E 4 HOH A 146 746 146 HOH HOH . E 4 HOH A 147 747 147 HOH HOH . E 4 HOH A 148 748 148 HOH HOH . E 4 HOH A 149 749 149 HOH HOH . E 4 HOH A 150 750 150 HOH HOH . E 4 HOH A 151 751 151 HOH HOH . E 4 HOH A 152 752 152 HOH HOH . E 4 HOH A 153 753 153 HOH HOH . E 4 HOH A 154 754 154 HOH HOH . E 4 HOH A 155 755 155 HOH HOH . E 4 HOH A 156 756 156 HOH HOH . E 4 HOH A 157 757 157 HOH HOH . E 4 HOH A 158 758 158 HOH HOH . E 4 HOH A 159 759 159 HOH HOH . E 4 HOH A 160 760 160 HOH HOH . E 4 HOH A 161 761 161 HOH HOH . E 4 HOH A 162 762 162 HOH HOH . E 4 HOH A 163 763 163 HOH HOH . E 4 HOH A 164 764 164 HOH HOH . E 4 HOH A 165 765 165 HOH HOH . E 4 HOH A 166 766 166 HOH HOH . E 4 HOH A 167 767 167 HOH HOH . E 4 HOH A 168 768 168 HOH HOH . E 4 HOH A 169 769 169 HOH HOH . E 4 HOH A 170 770 170 HOH HOH . E 4 HOH A 171 771 171 HOH HOH . E 4 HOH A 172 772 172 HOH HOH . E 4 HOH A 173 773 173 HOH HOH . E 4 HOH A 174 774 174 HOH HOH . E 4 HOH A 175 775 175 HOH HOH . E 4 HOH A 176 776 176 HOH HOH . E 4 HOH A 177 777 177 HOH HOH . E 4 HOH A 178 778 178 HOH HOH . E 4 HOH A 179 779 179 HOH HOH . E 4 HOH A 180 780 180 HOH HOH . E 4 HOH A 181 781 181 HOH HOH . E 4 HOH A 182 782 182 HOH HOH . E 4 HOH A 183 783 183 HOH HOH . E 4 HOH A 184 784 184 HOH HOH . E 4 HOH A 185 785 185 HOH HOH . E 4 HOH A 186 786 186 HOH HOH . E 4 HOH A 187 787 187 HOH HOH . E 4 HOH A 188 788 188 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 -3.759 31.31 10.417 0.8 28.27 ? P XMP 501 A 1 HETATM 2 O O1P XMP . . . B 2 -3.407 32.647 11.002 0.8 26.69 ? O1P XMP 501 A 1 HETATM 3 O O2P XMP . . . B 2 -2.692 30.245 10.655 0.8 27.39 ? O2P XMP 501 A 1 HETATM 4 O O5' XMP . . . B 2 -5.031 30.761 11.276 0.8 26.02 ? O5' XMP 501 A 1 HETATM 5 O O3P XMP . . . B 2 -4.219 31.389 8.953 0.8 32.36 ? O3P XMP 501 A 1 HETATM 6 C C5' XMP . . . B 2 -5.456 29.409 11.21 0.8 29.25 ? C5' XMP 501 A 1 HETATM 7 C C4' XMP . . . B 2 -6.624 29.267 12.181 0.8 28.75 ? C4' XMP 501 A 1 HETATM 8 O O4' XMP . . . B 2 -7.682 30.204 11.862 0.8 30.75 ? O4' XMP 501 A 1 HETATM 9 C C1' XMP . . . B 2 -8.878 29.66 12.409 0.8 30.78 ? C1' XMP 501 A 1 HETATM 10 N N9 XMP . . . B 2 -9.948 29.767 11.397 0.8 32.85 ? N9 XMP 501 A 1 HETATM 11 C C4 XMP . . . B 2 -10.612 30.887 11.155 0.8 33.33 ? C4 XMP 501 A 1 HETATM 12 N N3 XMP . . . B 2 -10.565 32.125 11.64 0.8 35.03 ? N3 XMP 501 A 1 HETATM 13 N N1 XMP . . . B 2 -12.315 32.817 10.197 0.8 38.68 ? N1 XMP 501 A 1 HETATM 14 C C2 XMP . . . B 2 -11.404 33.075 11.178 0.8 37.98 ? C2 XMP 501 A 1 HETATM 15 O O2 XMP . . . B 2 -11.292 34.245 11.63 0.8 38.42 ? O2 XMP 501 A 1 HETATM 16 C C6 XMP . . . B 2 -12.467 31.615 9.644 0.8 38.14 ? C6 XMP 501 A 1 HETATM 17 O O6 XMP . . . B 2 -13.322 31.335 8.759 0.8 41.72 ? O6 XMP 501 A 1 HETATM 18 C C5 XMP . . . B 2 -11.565 30.563 10.095 0.8 35.29 ? C5 XMP 501 A 1 HETATM 19 N N7 XMP . . . B 2 -11.421 29.276 9.828 0.8 37.34 ? N7 XMP 501 A 1 HETATM 20 C C8 XMP . . . B 2 -10.416 28.794 10.593 0.8 35.18 ? C8 XMP 501 A 1 HETATM 21 C C2' XMP . . . B 2 -8.591 28.231 12.911 0.8 30.12 ? C2' XMP 501 A 1 HETATM 22 O O2' XMP . . . B 2 -8.4 28.26 14.348 0.8 28.68 ? O2' XMP 501 A 1 HETATM 23 C C3' XMP . . . B 2 -7.302 27.888 12.167 0.8 28 ? C3' XMP 501 A 1 HETATM 24 O O3' XMP . . . B 2 -6.524 26.798 12.708 0.8 25.44 ? O3' XMP 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 24 #