data_8D1S # _model_server_result.job_id b-A-BUIv79ahzua5jFpQrA _model_server_result.datetime_utc '2024-11-21 20:47:48' _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 8d1s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8D1S # _exptl.entry_id 8D1S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 291.263 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile _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 8D1S _cell.length_a 84.377 _cell.length_b 84.377 _cell.length_c 292.492 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8D1S _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C12 H13 N5 O4' _chem_comp.formula_weight 291.263 _chem_comp.id TO1 _chem_comp.mon_nstd_flag . _chem_comp.name 4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile _chem_comp.type non-polymer _chem_comp.pdbx_synonyms TOYOCAMYCIN # 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 C N TO1 sing 310 n n C O TO1 sing 311 n n C C9 TO1 sing 312 n n N C2 TO1 sing 313 n y N C7 TO1 sing 314 n y O C11 TO1 sing 315 n n C2 N2 TO1 doub 316 n y C2 C5 TO1 sing 317 n y N2 C3 TO1 sing 318 n y O2 C9 TO1 sing 319 n n C3 N3 TO1 doub 320 n y N3 C4 TO1 sing 321 n y O3 C10 TO1 sing 322 n n C4 C5 TO1 doub 323 n y C4 N5 TO1 sing 324 n n N4 C8 TO1 trip 325 n n O4 C12 TO1 sing 326 n n C5 C6 TO1 sing 327 n y C6 C7 TO1 doub 328 n y C6 C8 TO1 sing 329 n n C9 C10 TO1 sing 330 n n C10 C11 TO1 sing 331 n n C11 C12 TO1 sing 332 n n C H TO1 sing 333 n n O2 HO2 TO1 sing 334 n n C3 H3 TO1 sing 335 n n O3 HO3 TO1 sing 336 n n O4 HO4 TO1 sing 337 n n N5 HN5 TO1 sing 338 n n N5 HN5A TO1 sing 339 n n C7 H7 TO1 sing 340 n n C9 H9 TO1 sing 341 n n C10 H10 TO1 sing 342 n n C11 H11 TO1 sing 343 n n C12 H12 TO1 sing 344 n n C12 H12A TO1 sing 345 n n # _atom_sites.entry_id 8D1S _atom_sites.fract_transf_matrix[1][1] 0.011852 _atom_sites.fract_transf_matrix[1][2] 0.006843 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013685 _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] 0.003419 _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 TO1 A 1 501 501 TO1 XXX . C 3 SO4 A 1 502 1 SO4 SO4 . D 3 SO4 A 1 503 2 SO4 SO4 . E 4 HOH A 1 601 170 HOH HOH . E 4 HOH A 2 602 197 HOH HOH . E 4 HOH A 3 603 288 HOH HOH . E 4 HOH A 4 604 185 HOH HOH . E 4 HOH A 5 605 186 HOH HOH . E 4 HOH A 6 606 212 HOH HOH . E 4 HOH A 7 607 80 HOH HOH . E 4 HOH A 8 608 26 HOH HOH . E 4 HOH A 9 609 75 HOH HOH . E 4 HOH A 10 610 195 HOH HOH . E 4 HOH A 11 611 106 HOH HOH . E 4 HOH A 12 612 276 HOH HOH . E 4 HOH A 13 613 28 HOH HOH . E 4 HOH A 14 614 125 HOH HOH . E 4 HOH A 15 615 161 HOH HOH . E 4 HOH A 16 616 202 HOH HOH . E 4 HOH A 17 617 3 HOH HOH . E 4 HOH A 18 618 144 HOH HOH . E 4 HOH A 19 619 56 HOH HOH . E 4 HOH A 20 620 290 HOH HOH . E 4 HOH A 21 621 190 HOH HOH . E 4 HOH A 22 622 171 HOH HOH . E 4 HOH A 23 623 142 HOH HOH . E 4 HOH A 24 624 78 HOH HOH . E 4 HOH A 25 625 163 HOH HOH . E 4 HOH A 26 626 9 HOH HOH . E 4 HOH A 27 627 307 HOH HOH . E 4 HOH A 28 628 208 HOH HOH . E 4 HOH A 29 629 151 HOH HOH . E 4 HOH A 30 630 107 HOH HOH . E 4 HOH A 31 631 86 HOH HOH . E 4 HOH A 32 632 291 HOH HOH . E 4 HOH A 33 633 262 HOH HOH . E 4 HOH A 34 634 89 HOH HOH . E 4 HOH A 35 635 74 HOH HOH . E 4 HOH A 36 636 137 HOH HOH . E 4 HOH A 37 637 88 HOH HOH . E 4 HOH A 38 638 41 HOH HOH . E 4 HOH A 39 639 94 HOH HOH . E 4 HOH A 40 640 22 HOH HOH . E 4 HOH A 41 641 32 HOH HOH . E 4 HOH A 42 642 100 HOH HOH . E 4 HOH A 43 643 245 HOH HOH . E 4 HOH A 44 644 11 HOH HOH . E 4 HOH A 45 645 131 HOH HOH . E 4 HOH A 46 646 119 HOH HOH . E 4 HOH A 47 647 116 HOH HOH . E 4 HOH A 48 648 192 HOH HOH . E 4 HOH A 49 649 174 HOH HOH . E 4 HOH A 50 650 111 HOH HOH . E 4 HOH A 51 651 84 HOH HOH . E 4 HOH A 52 652 157 HOH HOH . E 4 HOH A 53 653 110 HOH HOH . E 4 HOH A 54 654 18 HOH HOH . E 4 HOH A 55 655 263 HOH HOH . E 4 HOH A 56 656 254 HOH HOH . E 4 HOH A 57 657 43 HOH HOH . E 4 HOH A 58 658 93 HOH HOH . E 4 HOH A 59 659 55 HOH HOH . E 4 HOH A 60 660 13 HOH HOH . E 4 HOH A 61 661 58 HOH HOH . E 4 HOH A 62 662 115 HOH HOH . E 4 HOH A 63 663 36 HOH HOH . E 4 HOH A 64 664 103 HOH HOH . E 4 HOH A 65 665 148 HOH HOH . E 4 HOH A 66 666 140 HOH HOH . E 4 HOH A 67 667 105 HOH HOH . E 4 HOH A 68 668 34 HOH HOH . E 4 HOH A 69 669 5 HOH HOH . E 4 HOH A 70 670 322 HOH HOH . E 4 HOH A 71 671 48 HOH HOH . E 4 HOH A 72 672 67 HOH HOH . E 4 HOH A 73 673 62 HOH HOH . E 4 HOH A 74 674 83 HOH HOH . E 4 HOH A 75 675 241 HOH HOH . E 4 HOH A 76 676 6 HOH HOH . E 4 HOH A 77 677 166 HOH HOH . E 4 HOH A 78 678 198 HOH HOH . E 4 HOH A 79 679 31 HOH HOH . E 4 HOH A 80 680 156 HOH HOH . E 4 HOH A 81 681 97 HOH HOH . E 4 HOH A 82 682 68 HOH HOH . E 4 HOH A 83 683 200 HOH HOH . E 4 HOH A 84 684 211 HOH HOH . E 4 HOH A 85 685 37 HOH HOH . E 4 HOH A 86 686 99 HOH HOH . E 4 HOH A 87 687 12 HOH HOH . E 4 HOH A 88 688 30 HOH HOH . E 4 HOH A 89 689 145 HOH HOH . E 4 HOH A 90 690 130 HOH HOH . E 4 HOH A 91 691 203 HOH HOH . E 4 HOH A 92 692 51 HOH HOH . E 4 HOH A 93 693 191 HOH HOH . E 4 HOH A 94 694 53 HOH HOH . E 4 HOH A 95 695 29 HOH HOH . E 4 HOH A 96 696 238 HOH HOH . E 4 HOH A 97 697 175 HOH HOH . E 4 HOH A 98 698 66 HOH HOH . E 4 HOH A 99 699 54 HOH HOH . E 4 HOH A 100 700 225 HOH HOH . E 4 HOH A 101 701 150 HOH HOH . E 4 HOH A 102 702 8 HOH HOH . E 4 HOH A 103 703 35 HOH HOH . E 4 HOH A 104 704 7 HOH HOH . E 4 HOH A 105 705 317 HOH HOH . E 4 HOH A 106 706 297 HOH HOH . E 4 HOH A 107 707 79 HOH HOH . E 4 HOH A 108 708 20 HOH HOH . E 4 HOH A 109 709 220 HOH HOH . E 4 HOH A 110 710 158 HOH HOH . E 4 HOH A 111 711 179 HOH HOH . E 4 HOH A 112 712 182 HOH HOH . E 4 HOH A 113 713 10 HOH HOH . E 4 HOH A 114 714 188 HOH HOH . E 4 HOH A 115 715 117 HOH HOH . E 4 HOH A 116 716 234 HOH HOH . E 4 HOH A 117 717 332 HOH HOH . E 4 HOH A 118 718 52 HOH HOH . E 4 HOH A 119 719 201 HOH HOH . E 4 HOH A 120 720 40 HOH HOH . E 4 HOH A 121 721 104 HOH HOH . E 4 HOH A 122 722 61 HOH HOH . E 4 HOH A 123 723 240 HOH HOH . E 4 HOH A 124 724 252 HOH HOH . E 4 HOH A 125 725 14 HOH HOH . E 4 HOH A 126 726 135 HOH HOH . E 4 HOH A 127 727 42 HOH HOH . E 4 HOH A 128 728 65 HOH HOH . E 4 HOH A 129 729 4 HOH HOH . E 4 HOH A 130 730 162 HOH HOH . E 4 HOH A 131 731 147 HOH HOH . E 4 HOH A 132 732 155 HOH HOH . E 4 HOH A 133 733 81 HOH HOH . E 4 HOH A 134 734 69 HOH HOH . E 4 HOH A 135 735 316 HOH HOH . E 4 HOH A 136 736 17 HOH HOH . E 4 HOH A 137 737 44 HOH HOH . E 4 HOH A 138 738 247 HOH HOH . E 4 HOH A 139 739 85 HOH HOH . E 4 HOH A 140 740 189 HOH HOH . E 4 HOH A 141 741 46 HOH HOH . E 4 HOH A 142 742 126 HOH HOH . E 4 HOH A 143 743 77 HOH HOH . E 4 HOH A 144 744 15 HOH HOH . E 4 HOH A 145 745 59 HOH HOH . E 4 HOH A 146 746 39 HOH HOH . E 4 HOH A 147 747 169 HOH HOH . E 4 HOH A 148 748 160 HOH HOH . E 4 HOH A 149 749 71 HOH HOH . E 4 HOH A 150 750 138 HOH HOH . E 4 HOH A 151 751 96 HOH HOH . E 4 HOH A 152 752 121 HOH HOH . E 4 HOH A 153 753 63 HOH HOH . E 4 HOH A 154 754 246 HOH HOH . E 4 HOH A 155 755 164 HOH HOH . E 4 HOH A 156 756 133 HOH HOH . E 4 HOH A 157 757 108 HOH HOH . E 4 HOH A 158 758 344 HOH HOH . E 4 HOH A 159 759 49 HOH HOH . E 4 HOH A 160 760 283 HOH HOH . E 4 HOH A 161 761 128 HOH HOH . E 4 HOH A 162 762 352 HOH HOH . E 4 HOH A 163 763 102 HOH HOH . E 4 HOH A 164 764 294 HOH HOH . E 4 HOH A 165 765 231 HOH HOH . E 4 HOH A 166 766 64 HOH HOH . E 4 HOH A 167 767 95 HOH HOH . E 4 HOH A 168 768 19 HOH HOH . E 4 HOH A 169 769 214 HOH HOH . E 4 HOH A 170 770 114 HOH HOH . E 4 HOH A 171 771 353 HOH HOH . E 4 HOH A 172 772 152 HOH HOH . E 4 HOH A 173 773 91 HOH HOH . E 4 HOH A 174 774 60 HOH HOH . E 4 HOH A 175 775 23 HOH HOH . E 4 HOH A 176 776 342 HOH HOH . E 4 HOH A 177 777 183 HOH HOH . E 4 HOH A 178 778 149 HOH HOH . E 4 HOH A 179 779 21 HOH HOH . E 4 HOH A 180 780 73 HOH HOH . E 4 HOH A 181 781 168 HOH HOH . E 4 HOH A 182 782 143 HOH HOH . E 4 HOH A 183 783 226 HOH HOH . E 4 HOH A 184 784 16 HOH HOH . E 4 HOH A 185 785 272 HOH HOH . E 4 HOH A 186 786 92 HOH HOH . E 4 HOH A 187 787 87 HOH HOH . E 4 HOH A 188 788 141 HOH HOH . E 4 HOH A 189 789 98 HOH HOH . E 4 HOH A 190 790 286 HOH HOH . E 4 HOH A 191 791 216 HOH HOH . E 4 HOH A 192 792 146 HOH HOH . E 4 HOH A 193 793 306 HOH HOH . E 4 HOH A 194 794 38 HOH HOH . E 4 HOH A 195 795 27 HOH HOH . E 4 HOH A 196 796 47 HOH HOH . E 4 HOH A 197 797 337 HOH HOH . E 4 HOH A 198 798 120 HOH HOH . E 4 HOH A 199 799 273 HOH HOH . E 4 HOH A 200 800 321 HOH HOH . E 4 HOH A 201 801 311 HOH HOH . E 4 HOH A 202 802 264 HOH HOH . E 4 HOH A 203 803 253 HOH HOH . E 4 HOH A 204 804 206 HOH HOH . E 4 HOH A 205 805 57 HOH HOH . E 4 HOH A 206 806 310 HOH HOH . E 4 HOH A 207 807 113 HOH HOH . E 4 HOH A 208 808 181 HOH HOH . E 4 HOH A 209 809 139 HOH HOH . E 4 HOH A 210 810 153 HOH HOH . E 4 HOH A 211 811 112 HOH HOH . E 4 HOH A 212 812 303 HOH HOH . E 4 HOH A 213 813 312 HOH HOH . E 4 HOH A 214 814 271 HOH HOH . E 4 HOH A 215 815 228 HOH HOH . E 4 HOH A 216 816 134 HOH HOH . E 4 HOH A 217 817 269 HOH HOH . E 4 HOH A 218 818 210 HOH HOH . E 4 HOH A 219 819 207 HOH HOH . E 4 HOH A 220 820 193 HOH HOH . E 4 HOH A 221 821 265 HOH HOH . E 4 HOH A 222 822 257 HOH HOH . E 4 HOH A 223 823 118 HOH HOH . E 4 HOH A 224 824 293 HOH HOH . E 4 HOH A 225 825 25 HOH HOH . E 4 HOH A 226 826 50 HOH HOH . E 4 HOH A 227 827 270 HOH HOH . E 4 HOH A 228 828 90 HOH HOH . E 4 HOH A 229 829 323 HOH HOH . E 4 HOH A 230 830 261 HOH HOH . E 4 HOH A 231 831 176 HOH HOH . E 4 HOH A 232 832 301 HOH HOH . E 4 HOH A 233 833 308 HOH HOH . E 4 HOH A 234 834 242 HOH HOH . E 4 HOH A 235 835 199 HOH HOH . E 4 HOH A 236 836 313 HOH HOH . E 4 HOH A 237 837 320 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 C C TO1 . . . B 2 17.207 9.518 11.606 1 30.13 ? C TO1 501 A 1 HETATM 2 N N TO1 . . . B 2 17.271 8.066 11.505 1 31.49 ? N TO1 501 A 1 HETATM 3 O O TO1 . . . B 2 16.906 10.066 10.339 1 28.98 ? O TO1 501 A 1 HETATM 4 C C2 TO1 . . . B 2 16.579 7.194 12.312 1 29.77 ? C2 TO1 501 A 1 HETATM 5 N N2 TO1 . . . B 2 15.651 7.54 13.197 1 24.57 ? N2 TO1 501 A 1 HETATM 6 O O2 TO1 . . . B 2 18.663 9.95 13.421 1 27.94 ? O2 TO1 501 A 1 HETATM 7 C C3 TO1 . . . B 2 15.118 6.478 13.81 1 27.55 ? C3 TO1 501 A 1 HETATM 8 N N3 TO1 . . . B 2 15.395 5.19 13.638 1 26.04 ? N3 TO1 501 A 1 HETATM 9 O O3 TO1 . . . B 2 17.658 12.4 12.498 1 28.45 ? O3 TO1 501 A 1 HETATM 10 C C4 TO1 . . . B 2 16.362 4.848 12.746 1 30.7 ? C4 TO1 501 A 1 HETATM 11 N N4 TO1 . . . B 2 19.465 4.048 10.177 1 48.84 ? N4 TO1 501 A 1 HETATM 12 O O4 TO1 . . . B 2 19.211 10.644 8.857 1 35.83 ? O4 TO1 501 A 1 HETATM 13 C C5 TO1 . . . B 2 16.995 5.876 12.012 1 30.46 ? C5 TO1 501 A 1 HETATM 14 N N5 TO1 . . . B 2 16.692 3.559 12.637 1 26.69 ? N5 TO1 501 A 1 HETATM 15 C C6 TO1 . . . B 2 17.972 5.991 10.964 1 36.77 ? C6 TO1 501 A 1 HETATM 16 C C7 TO1 . . . B 2 18.09 7.328 10.67 1 29.48 ? C7 TO1 501 A 1 HETATM 17 C C8 TO1 . . . B 2 18.809 4.925 10.488 1 47.28 ? C8 TO1 501 A 1 HETATM 18 C C9 TO1 . . . B 2 18.54 10.145 12.021 1 31.67 ? C9 TO1 501 A 1 HETATM 19 C C10 TO1 . . . B 2 18.337 11.591 11.534 1 29.64 ? C10 TO1 501 A 1 HETATM 20 C C11 TO1 . . . B 2 17.437 11.41 10.291 1 30.78 ? C11 TO1 501 A 1 HETATM 21 C C12 TO1 . . . B 2 18.145 11.602 8.981 1 30.23 ? C12 TO1 501 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 26 _model_server_stats.element_count 21 #