data_6P78 # _model_server_result.job_id 7xyQJ_7lEYVvJnx0rGEiaQ _model_server_result.datetime_utc '2024-10-19 19:33:16' _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 6p78 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 6P78 # _exptl.entry_id 6P78 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 277.279 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-amino-5-({[(1S,4S,5S)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one _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 6P78 _cell.length_a 57.606 _cell.length_b 57.606 _cell.length_c 152.414 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6P78 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _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 3 _struct_asym.id C _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 metalc ? metalc1 A SG CYS 45 A CYS 23 1_555 B FE1 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc2 A SG CYS 50 A CYS 28 1_555 B FE3 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc3 A SG CYS 53 A CYS 31 1_555 B FE4 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? covale ? covale1 A C PRO 175 A PRO 153 1_555 A N SMC 176 A SMC 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C SMC 176 A SMC 154 1_555 A N LEU 177 A LEU 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc4 B FE2 SF4 . A SF4 501 1_555 D OXT SAM . A SAM 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc5 B FE2 SF4 . A SF4 501 1_555 D N SAM . A SAM 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? # _chem_comp.formula 'C12 H15 N5 O3' _chem_comp.formula_weight 277.279 _chem_comp.id QUG _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-5-({[(1S,4S,5S)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Queuine # _atom_sites.entry_id 6P78 _atom_sites.fract_transf_matrix[1][1] 0.017359 _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] 0.017359 _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] 0.006561 _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 SF4 A 1 501 501 SF4 SF4 . C 3 QUG A 1 502 504 QUG quG . D 4 SAM A 1 503 601 SAM SAM . E 5 HOH A 1 601 125 HOH HOH . E 5 HOH A 2 602 65 HOH HOH . E 5 HOH A 3 603 221 HOH HOH . E 5 HOH A 4 604 164 HOH HOH . E 5 HOH A 5 605 119 HOH HOH . E 5 HOH A 6 606 169 HOH HOH . E 5 HOH A 7 607 108 HOH HOH . E 5 HOH A 8 608 183 HOH HOH . E 5 HOH A 9 609 34 HOH HOH . E 5 HOH A 10 610 78 HOH HOH . E 5 HOH A 11 611 94 HOH HOH . E 5 HOH A 12 612 105 HOH HOH . E 5 HOH A 13 613 242 HOH HOH . E 5 HOH A 14 614 241 HOH HOH . E 5 HOH A 15 615 43 HOH HOH . E 5 HOH A 16 616 58 HOH HOH . E 5 HOH A 17 617 230 HOH HOH . E 5 HOH A 18 618 202 HOH HOH . E 5 HOH A 19 619 13 HOH HOH . E 5 HOH A 20 620 47 HOH HOH . E 5 HOH A 21 621 46 HOH HOH . E 5 HOH A 22 622 236 HOH HOH . E 5 HOH A 23 623 118 HOH HOH . E 5 HOH A 24 624 156 HOH HOH . E 5 HOH A 25 625 41 HOH HOH . E 5 HOH A 26 626 147 HOH HOH . E 5 HOH A 27 627 176 HOH HOH . E 5 HOH A 28 628 26 HOH HOH . E 5 HOH A 29 629 146 HOH HOH . E 5 HOH A 30 630 1 HOH HOH . E 5 HOH A 31 631 7 HOH HOH . E 5 HOH A 32 632 240 HOH HOH . E 5 HOH A 33 633 117 HOH HOH . E 5 HOH A 34 634 128 HOH HOH . E 5 HOH A 35 635 35 HOH HOH . E 5 HOH A 36 636 23 HOH HOH . E 5 HOH A 37 637 189 HOH HOH . E 5 HOH A 38 638 163 HOH HOH . E 5 HOH A 39 639 9 HOH HOH . E 5 HOH A 40 640 246 HOH HOH . E 5 HOH A 41 641 79 HOH HOH . E 5 HOH A 42 642 190 HOH HOH . E 5 HOH A 43 643 10 HOH HOH . E 5 HOH A 44 644 4 HOH HOH . E 5 HOH A 45 645 68 HOH HOH . E 5 HOH A 46 646 121 HOH HOH . E 5 HOH A 47 647 143 HOH HOH . E 5 HOH A 48 648 57 HOH HOH . E 5 HOH A 49 649 53 HOH HOH . E 5 HOH A 50 650 100 HOH HOH . E 5 HOH A 51 651 113 HOH HOH . E 5 HOH A 52 652 203 HOH HOH . E 5 HOH A 53 653 97 HOH HOH . E 5 HOH A 54 654 15 HOH HOH . E 5 HOH A 55 655 218 HOH HOH . E 5 HOH A 56 656 153 HOH HOH . E 5 HOH A 57 657 130 HOH HOH . E 5 HOH A 58 658 201 HOH HOH . E 5 HOH A 59 659 20 HOH HOH . E 5 HOH A 60 660 55 HOH HOH . E 5 HOH A 61 661 84 HOH HOH . E 5 HOH A 62 662 69 HOH HOH . E 5 HOH A 63 663 132 HOH HOH . E 5 HOH A 64 664 19 HOH HOH . E 5 HOH A 65 665 92 HOH HOH . E 5 HOH A 66 666 6 HOH HOH . E 5 HOH A 67 667 2 HOH HOH . E 5 HOH A 68 668 98 HOH HOH . E 5 HOH A 69 669 63 HOH HOH . E 5 HOH A 70 670 33 HOH HOH . E 5 HOH A 71 671 71 HOH HOH . E 5 HOH A 72 672 37 HOH HOH . E 5 HOH A 73 673 112 HOH HOH . E 5 HOH A 74 674 142 HOH HOH . E 5 HOH A 75 675 75 HOH HOH . E 5 HOH A 76 676 181 HOH HOH . E 5 HOH A 77 677 51 HOH HOH . E 5 HOH A 78 678 150 HOH HOH . E 5 HOH A 79 679 186 HOH HOH . E 5 HOH A 80 680 56 HOH HOH . E 5 HOH A 81 681 106 HOH HOH . E 5 HOH A 82 682 14 HOH HOH . E 5 HOH A 83 683 80 HOH HOH . E 5 HOH A 84 684 155 HOH HOH . E 5 HOH A 85 685 209 HOH HOH . E 5 HOH A 86 686 127 HOH HOH . E 5 HOH A 87 687 86 HOH HOH . E 5 HOH A 88 688 30 HOH HOH . E 5 HOH A 89 689 21 HOH HOH . E 5 HOH A 90 690 136 HOH HOH . E 5 HOH A 91 691 48 HOH HOH . E 5 HOH A 92 692 167 HOH HOH . E 5 HOH A 93 693 157 HOH HOH . E 5 HOH A 94 694 228 HOH HOH . E 5 HOH A 95 695 85 HOH HOH . E 5 HOH A 96 696 40 HOH HOH . E 5 HOH A 97 697 166 HOH HOH . E 5 HOH A 98 698 3 HOH HOH . E 5 HOH A 99 699 96 HOH HOH . E 5 HOH A 100 700 139 HOH HOH . E 5 HOH A 101 701 39 HOH HOH . E 5 HOH A 102 702 42 HOH HOH . E 5 HOH A 103 703 101 HOH HOH . E 5 HOH A 104 704 8 HOH HOH . E 5 HOH A 105 705 107 HOH HOH . E 5 HOH A 106 706 111 HOH HOH . E 5 HOH A 107 707 27 HOH HOH . E 5 HOH A 108 708 16 HOH HOH . E 5 HOH A 109 709 73 HOH HOH . E 5 HOH A 110 710 231 HOH HOH . E 5 HOH A 111 711 64 HOH HOH . E 5 HOH A 112 712 134 HOH HOH . E 5 HOH A 113 713 60 HOH HOH . E 5 HOH A 114 714 22 HOH HOH . E 5 HOH A 115 715 24 HOH HOH . E 5 HOH A 116 716 244 HOH HOH . E 5 HOH A 117 717 144 HOH HOH . E 5 HOH A 118 718 36 HOH HOH . E 5 HOH A 119 719 70 HOH HOH . E 5 HOH A 120 720 18 HOH HOH . E 5 HOH A 121 721 5 HOH HOH . E 5 HOH A 122 722 151 HOH HOH . E 5 HOH A 123 723 44 HOH HOH . E 5 HOH A 124 724 87 HOH HOH . E 5 HOH A 125 725 123 HOH HOH . E 5 HOH A 126 726 12 HOH HOH . E 5 HOH A 127 727 77 HOH HOH . E 5 HOH A 128 728 32 HOH HOH . E 5 HOH A 129 729 49 HOH HOH . E 5 HOH A 130 730 54 HOH HOH . E 5 HOH A 131 731 122 HOH HOH . E 5 HOH A 132 732 25 HOH HOH . E 5 HOH A 133 733 45 HOH HOH . E 5 HOH A 134 734 129 HOH HOH . E 5 HOH A 135 735 74 HOH HOH . E 5 HOH A 136 736 11 HOH HOH . E 5 HOH A 137 737 138 HOH HOH . E 5 HOH A 138 738 141 HOH HOH . E 5 HOH A 139 739 115 HOH HOH . E 5 HOH A 140 740 223 HOH HOH . E 5 HOH A 141 741 110 HOH HOH . E 5 HOH A 142 742 104 HOH HOH . E 5 HOH A 143 743 90 HOH HOH . E 5 HOH A 144 744 184 HOH HOH . E 5 HOH A 145 745 50 HOH HOH . E 5 HOH A 146 746 82 HOH HOH . E 5 HOH A 147 747 52 HOH HOH . E 5 HOH A 148 748 67 HOH HOH . E 5 HOH A 149 749 212 HOH HOH . E 5 HOH A 150 750 116 HOH HOH . E 5 HOH A 151 751 179 HOH HOH . E 5 HOH A 152 752 59 HOH HOH . E 5 HOH A 153 753 91 HOH HOH . E 5 HOH A 154 754 103 HOH HOH . E 5 HOH A 155 755 124 HOH HOH . E 5 HOH A 156 756 220 HOH HOH . E 5 HOH A 157 757 204 HOH HOH . E 5 HOH A 158 758 66 HOH HOH . E 5 HOH A 159 759 217 HOH HOH . E 5 HOH A 160 760 95 HOH HOH . E 5 HOH A 161 761 224 HOH HOH . E 5 HOH A 162 762 109 HOH HOH . E 5 HOH A 163 763 28 HOH HOH . E 5 HOH A 164 764 222 HOH HOH . E 5 HOH A 165 765 191 HOH HOH . E 5 HOH A 166 766 193 HOH HOH . E 5 HOH A 167 767 114 HOH HOH . E 5 HOH A 168 768 29 HOH HOH . E 5 HOH A 169 769 145 HOH HOH . E 5 HOH A 170 770 215 HOH HOH . E 5 HOH A 171 771 195 HOH HOH . E 5 HOH A 172 772 149 HOH HOH . E 5 HOH A 173 773 88 HOH HOH . E 5 HOH A 174 774 161 HOH HOH . E 5 HOH A 175 775 237 HOH HOH . E 5 HOH A 176 776 137 HOH HOH . E 5 HOH A 177 777 76 HOH HOH . E 5 HOH A 178 778 31 HOH HOH . E 5 HOH A 179 779 174 HOH HOH . E 5 HOH A 180 780 177 HOH HOH . E 5 HOH A 181 781 89 HOH HOH . E 5 HOH A 182 782 211 HOH HOH . E 5 HOH A 183 783 62 HOH HOH . E 5 HOH A 184 784 135 HOH HOH . E 5 HOH A 185 785 154 HOH HOH . E 5 HOH A 186 786 72 HOH HOH . E 5 HOH A 187 787 83 HOH HOH . E 5 HOH A 188 788 170 HOH HOH . E 5 HOH A 189 789 38 HOH HOH . E 5 HOH A 190 790 197 HOH HOH . E 5 HOH A 191 791 233 HOH HOH . E 5 HOH A 192 792 160 HOH HOH . E 5 HOH A 193 793 152 HOH HOH . E 5 HOH A 194 794 199 HOH HOH . E 5 HOH A 195 795 81 HOH HOH . E 5 HOH A 196 796 126 HOH HOH . E 5 HOH A 197 797 185 HOH HOH . E 5 HOH A 198 798 102 HOH HOH . E 5 HOH A 199 799 158 HOH HOH . E 5 HOH A 200 800 175 HOH HOH . E 5 HOH A 201 801 131 HOH HOH . E 5 HOH A 202 802 17 HOH HOH . E 5 HOH A 203 803 178 HOH HOH . E 5 HOH A 204 804 148 HOH HOH . E 5 HOH A 205 805 99 HOH HOH . E 5 HOH A 206 806 172 HOH HOH . E 5 HOH A 207 807 61 HOH HOH . E 5 HOH A 208 808 120 HOH HOH . E 5 HOH A 209 809 226 HOH HOH . E 5 HOH A 210 810 229 HOH HOH . E 5 HOH A 211 811 214 HOH HOH . E 5 HOH A 212 812 93 HOH HOH . E 5 HOH A 213 813 180 HOH HOH . E 5 HOH A 214 814 208 HOH HOH . E 5 HOH A 215 815 162 HOH HOH . E 5 HOH A 216 816 159 HOH HOH . E 5 HOH A 217 817 187 HOH HOH . E 5 HOH A 218 818 133 HOH HOH . E 5 HOH A 219 819 207 HOH HOH . E 5 HOH A 220 820 173 HOH HOH . E 5 HOH A 221 821 168 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 N QUG . . . C 3 3.354 43.776 74.638 1 25.76 ? N QUG 502 A 1 HETATM 2 C C QUG . . . C 3 2.144 44.094 75.149 1 26.49 ? C QUG 502 A 1 HETATM 3 O O QUG . . . C 3 6.475 40.855 71.094 1 53.1 ? O QUG 502 A 1 HETATM 4 C C1 QUG . . . C 3 3.657 42.542 74.208 1 24.95 ? C1 QUG 502 A 1 HETATM 5 C C10 QUG . . . C 3 6.013 37.494 70.38 1 43.09 ? C10 QUG 502 A 1 HETATM 6 C C11 QUG . . . C 3 3.522 39.155 73.49 1 29.89 ? C11 QUG 502 A 1 HETATM 7 C C2 QUG . . . C 3 2.609 41.509 74.359 1 22.61 ? C2 QUG 502 A 1 HETATM 8 C C3 QUG . . . C 3 1.309 41.908 74.928 1 26.98 ? C3 QUG 502 A 1 HETATM 9 C C4 QUG . . . C 3 1.189 39.739 74.465 1 24 ? C4 QUG 502 A 1 HETATM 10 C C5 QUG . . . C 3 2.48 40.079 74.075 1 26.73 ? C5 QUG 502 A 1 HETATM 11 C C6 QUG . . . C 3 7.045 38.6 70.366 1 47.58 ? C6 QUG 502 A 1 HETATM 12 C C7 QUG . . . C 3 6.671 39.507 71.532 1 50.57 ? C7 QUG 502 A 1 HETATM 13 C C8 QUG . . . C 3 5.455 38.871 72.215 1 42.26 ? C8 QUG 502 A 1 HETATM 14 C C9 QUG . . . C 3 5.146 37.637 71.385 1 40.2 ? C9 QUG 502 A 1 HETATM 15 N N1 QUG . . . C 3 1.123 43.2 75.301 1 26.65 ? N1 QUG 502 A 1 HETATM 16 N N2 QUG . . . C 3 0.528 40.819 74.952 1 28.02 ? N2 QUG 502 A 1 HETATM 17 N N3 QUG . . . C 3 4.278 39.763 72.378 1 34.56 ? N3 QUG 502 A 1 HETATM 18 N N4 QUG . . . C 3 1.933 45.384 75.527 1 30.71 ? N4 QUG 502 A 1 HETATM 19 O O1 QUG . . . C 3 8.354 38.105 70.658 1 41.66 ? O1 QUG 502 A 1 HETATM 20 O O2 QUG . . . C 3 4.782 42.28 73.742 1 28.79 ? O2 QUG 502 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 227 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #