data_1S3F # _model_server_result.job_id aR3bukOSnWWOOjTmWrmy7Q _model_server_result.datetime_utc '2024-12-04 17:53:12' _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 1s3f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":746}' # _entry.id 1S3F # _exptl.entry_id 1S3F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.187 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 9-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YL)-1,9-DIHYDRO-PURINE-6-THIONE _entity.pdbx_number_of_molecules 3 _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 1S3F _cell.length_a 79.582 _cell.length_b 79.582 _cell.length_c 185.727 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1S3F _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,PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C10 H12 N4 O4 Se' _chem_comp.formula_weight 331.187 _chem_comp.id SNI _chem_comp.mon_nstd_flag . _chem_comp.name 9-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YL)-1,9-DIHYDRO-PURINE-6-THIONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SELENOINOSINE # 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 O5' C5' SNI sing 290 n n O5' H5' SNI sing 291 n n C5' C4' SNI sing 292 n n C5' "H5'1" SNI sing 293 n n C5' "H5'2" SNI sing 294 n n C4' O4' SNI sing 295 n n C4' C3' SNI sing 296 n n C4' H4' SNI sing 297 n n O4' C1' SNI sing 298 n n C1' N9 SNI sing 299 n n C1' C2' SNI sing 300 n n C1' H1' SNI sing 301 n n N9 C4 SNI sing 302 n y N9 C8 SNI sing 303 n y C4 N3 SNI sing 304 n y C4 C5 SNI doub 305 n y N3 C2 SNI doub 306 n y C2 N1 SNI sing 307 n y C2 H2 SNI sing 308 n n N1 C6 SNI sing 309 n y N1 HN1 SNI sing 310 n n C6 SE SNI doub 311 n n C6 C5 SNI sing 312 n y C5 N7 SNI sing 313 n y N7 C8 SNI doub 314 n y C8 H8 SNI sing 315 n n C2' O2' SNI sing 316 n n C2' C3' SNI sing 317 n n C2' H2' SNI sing 318 n n O2' H1 SNI sing 319 n n C3' O3' SNI sing 320 n n C3' H3' SNI sing 321 n n O3' H3 SNI sing 322 n n # _atom_sites.entry_id 1S3F _atom_sites.fract_transf_matrix[1][1] 0.012566 _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] 0.012566 _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] 0.005384 _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 D 2 SNI A 1 745 745 SNI INO . E 2 SNI B 1 746 745 SNI INO . F 2 SNI C 1 747 745 SNI INO . G 3 HOH A 1 746 4 HOH TIP . G 3 HOH A 2 747 8 HOH TIP . G 3 HOH A 3 748 9 HOH TIP . G 3 HOH A 4 749 11 HOH TIP . G 3 HOH A 5 750 17 HOH TIP . G 3 HOH A 6 751 18 HOH TIP . G 3 HOH A 7 752 19 HOH TIP . G 3 HOH A 8 753 30 HOH TIP . G 3 HOH A 9 754 32 HOH TIP . G 3 HOH A 10 755 35 HOH TIP . G 3 HOH A 11 756 39 HOH TIP . G 3 HOH A 12 757 43 HOH TIP . G 3 HOH A 13 758 44 HOH TIP . G 3 HOH A 14 759 54 HOH TIP . G 3 HOH A 15 760 55 HOH TIP . G 3 HOH A 16 761 58 HOH TIP . G 3 HOH A 17 762 60 HOH TIP . G 3 HOH A 18 763 62 HOH TIP . G 3 HOH A 19 764 68 HOH TIP . G 3 HOH A 20 765 74 HOH TIP . G 3 HOH A 21 766 79 HOH TIP . G 3 HOH A 22 767 85 HOH TIP . G 3 HOH A 23 768 86 HOH TIP . G 3 HOH A 24 769 91 HOH TIP . G 3 HOH A 25 770 93 HOH TIP . G 3 HOH A 26 771 94 HOH TIP . G 3 HOH A 27 772 99 HOH TIP . G 3 HOH A 28 773 101 HOH TIP . G 3 HOH A 29 774 102 HOH TIP . G 3 HOH A 30 775 105 HOH TIP . G 3 HOH A 31 776 106 HOH TIP . G 3 HOH A 32 777 107 HOH TIP . G 3 HOH A 33 778 114 HOH TIP . G 3 HOH A 34 779 116 HOH TIP . G 3 HOH A 35 780 118 HOH TIP . G 3 HOH A 36 781 119 HOH TIP . G 3 HOH A 37 782 122 HOH TIP . G 3 HOH A 38 783 124 HOH TIP . G 3 HOH A 39 784 128 HOH TIP . G 3 HOH A 40 785 133 HOH TIP . G 3 HOH A 41 786 137 HOH TIP . G 3 HOH A 42 787 139 HOH TIP . G 3 HOH A 43 788 143 HOH TIP . G 3 HOH A 44 789 149 HOH TIP . G 3 HOH A 45 790 151 HOH TIP . G 3 HOH A 46 791 152 HOH TIP . G 3 HOH A 47 792 155 HOH TIP . G 3 HOH A 48 793 156 HOH TIP . G 3 HOH A 49 794 161 HOH TIP . G 3 HOH A 50 795 162 HOH TIP . H 3 HOH B 1 747 1 HOH TIP . H 3 HOH B 2 748 2 HOH TIP . H 3 HOH B 3 749 3 HOH TIP . H 3 HOH B 4 750 6 HOH TIP . H 3 HOH B 5 751 7 HOH TIP . H 3 HOH B 6 752 10 HOH TIP . H 3 HOH B 7 753 20 HOH TIP . H 3 HOH B 8 754 21 HOH TIP . H 3 HOH B 9 755 23 HOH TIP . H 3 HOH B 10 756 25 HOH TIP . H 3 HOH B 11 757 26 HOH TIP . H 3 HOH B 12 758 27 HOH TIP . H 3 HOH B 13 759 29 HOH TIP . H 3 HOH B 14 760 31 HOH TIP . H 3 HOH B 15 761 33 HOH TIP . H 3 HOH B 16 762 37 HOH TIP . H 3 HOH B 17 763 38 HOH TIP . H 3 HOH B 18 764 42 HOH TIP . H 3 HOH B 19 765 45 HOH TIP . H 3 HOH B 20 766 46 HOH TIP . H 3 HOH B 21 767 47 HOH TIP . H 3 HOH B 22 768 48 HOH TIP . H 3 HOH B 23 769 49 HOH TIP . H 3 HOH B 24 770 51 HOH TIP . H 3 HOH B 25 771 52 HOH TIP . H 3 HOH B 26 772 56 HOH TIP . H 3 HOH B 27 773 57 HOH TIP . H 3 HOH B 28 774 59 HOH TIP . H 3 HOH B 29 775 61 HOH TIP . H 3 HOH B 30 776 64 HOH TIP . H 3 HOH B 31 777 65 HOH TIP . H 3 HOH B 32 778 66 HOH TIP . H 3 HOH B 33 779 67 HOH TIP . H 3 HOH B 34 780 70 HOH TIP . H 3 HOH B 35 781 71 HOH TIP . H 3 HOH B 36 782 75 HOH TIP . H 3 HOH B 37 783 77 HOH TIP . H 3 HOH B 38 784 78 HOH TIP . H 3 HOH B 39 785 80 HOH TIP . H 3 HOH B 40 786 81 HOH TIP . H 3 HOH B 41 787 82 HOH TIP . H 3 HOH B 42 788 84 HOH TIP . H 3 HOH B 43 789 87 HOH TIP . H 3 HOH B 44 790 90 HOH TIP . H 3 HOH B 45 791 92 HOH TIP . H 3 HOH B 46 792 100 HOH TIP . H 3 HOH B 47 793 104 HOH TIP . H 3 HOH B 48 794 108 HOH TIP . H 3 HOH B 49 795 109 HOH TIP . H 3 HOH B 50 796 110 HOH TIP . H 3 HOH B 51 797 112 HOH TIP . H 3 HOH B 52 798 113 HOH TIP . H 3 HOH B 53 799 120 HOH TIP . H 3 HOH B 54 800 125 HOH TIP . H 3 HOH B 55 801 129 HOH TIP . H 3 HOH B 56 802 131 HOH TIP . H 3 HOH B 57 803 132 HOH TIP . H 3 HOH B 58 804 140 HOH TIP . H 3 HOH B 59 805 146 HOH TIP . H 3 HOH B 60 806 147 HOH TIP . H 3 HOH B 61 807 153 HOH TIP . H 3 HOH B 62 808 154 HOH TIP . H 3 HOH B 63 809 157 HOH TIP . I 3 HOH C 1 748 5 HOH TIP . I 3 HOH C 2 749 12 HOH TIP . I 3 HOH C 3 750 13 HOH TIP . I 3 HOH C 4 751 14 HOH TIP . I 3 HOH C 5 752 15 HOH TIP . I 3 HOH C 6 753 16 HOH TIP . I 3 HOH C 7 754 22 HOH TIP . I 3 HOH C 8 755 24 HOH TIP . I 3 HOH C 9 756 28 HOH TIP . I 3 HOH C 10 757 34 HOH TIP . I 3 HOH C 11 758 36 HOH TIP . I 3 HOH C 12 759 40 HOH TIP . I 3 HOH C 13 760 41 HOH TIP . I 3 HOH C 14 761 50 HOH TIP . I 3 HOH C 15 762 53 HOH TIP . I 3 HOH C 16 763 63 HOH TIP . I 3 HOH C 17 764 69 HOH TIP . I 3 HOH C 18 765 72 HOH TIP . I 3 HOH C 19 766 73 HOH TIP . I 3 HOH C 20 767 76 HOH TIP . I 3 HOH C 21 768 83 HOH TIP . I 3 HOH C 22 769 88 HOH TIP . I 3 HOH C 23 770 89 HOH TIP . I 3 HOH C 24 771 95 HOH TIP . I 3 HOH C 25 772 96 HOH TIP . I 3 HOH C 26 773 97 HOH TIP . I 3 HOH C 27 774 98 HOH TIP . I 3 HOH C 28 775 103 HOH TIP . I 3 HOH C 29 776 111 HOH TIP . I 3 HOH C 30 777 115 HOH TIP . I 3 HOH C 31 778 117 HOH TIP . I 3 HOH C 32 779 121 HOH TIP . I 3 HOH C 33 780 123 HOH TIP . I 3 HOH C 34 781 126 HOH TIP . I 3 HOH C 35 782 127 HOH TIP . I 3 HOH C 36 783 130 HOH TIP . I 3 HOH C 37 784 134 HOH TIP . I 3 HOH C 38 785 135 HOH TIP . I 3 HOH C 39 786 136 HOH TIP . I 3 HOH C 40 787 138 HOH TIP . I 3 HOH C 41 788 141 HOH TIP . I 3 HOH C 42 789 142 HOH TIP . I 3 HOH C 43 790 144 HOH TIP . I 3 HOH C 44 791 145 HOH TIP . I 3 HOH C 45 792 148 HOH TIP . I 3 HOH C 46 793 150 HOH TIP . I 3 HOH C 47 794 158 HOH TIP . I 3 HOH C 48 795 159 HOH TIP . I 3 HOH C 49 796 160 HOH TIP . # 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 O O5' SNI . . . E 2 8.277 19.889 1.24 1 39.38 ? O5' SNI 746 B 1 HETATM 2 C C5' SNI . . . E 2 7.421 19.977 0.113 1 39.82 ? C5' SNI 746 B 1 HETATM 3 C C4' SNI . . . E 2 6.106 19.201 0.358 1 38.98 ? C4' SNI 746 B 1 HETATM 4 O O4' SNI . . . E 2 5.699 18.88 1.52 1 38.17 ? O4' SNI 746 B 1 HETATM 5 C C1' SNI . . . E 2 4.509 19.405 2.154 1 38.5 ? C1' SNI 746 B 1 HETATM 6 N N9 SNI . . . E 2 4.476 20.319 3.303 1 37.25 ? N9 SNI 746 B 1 HETATM 7 C C4 SNI . . . E 2 3.428 21.048 3.865 1 37.01 ? C4 SNI 746 B 1 HETATM 8 N N3 SNI . . . E 2 2.089 21.038 3.494 1 36.06 ? N3 SNI 746 B 1 HETATM 9 C C2 SNI . . . E 2 1.248 21.856 4.22 1 36 ? C2 SNI 746 B 1 HETATM 10 N N1 SNI . . . E 2 1.752 22.674 5.244 1 36.7 ? N1 SNI 746 B 1 HETATM 11 C C6 SNI . . . E 2 3.114 22.736 5.656 1 37.46 ? C6 SNI 746 B 1 HETATM 12 SE SE SNI . . . E 2 3.444 23.527 6.574 1 38.23 ? SE SNI 746 B 1 HETATM 13 C C5 SNI . . . E 2 3.977 21.825 4.908 1 37.3 ? C5 SNI 746 B 1 HETATM 14 N N7 SNI . . . E 2 5.335 21.554 5.021 1 36.89 ? N7 SNI 746 B 1 HETATM 15 C C8 SNI . . . E 2 5.624 20.618 4.05 1 36.68 ? C8 SNI 746 B 1 HETATM 16 C C2' SNI . . . E 2 3.759 19.71 0.818 1 38.05 ? C2' SNI 746 B 1 HETATM 17 O O2' SNI . . . E 2 2.763 18.713 0.562 1 38.28 ? O2' SNI 746 B 1 HETATM 18 C C3' SNI . . . E 2 4.864 19.826 -0.292 1 37.98 ? C3' SNI 746 B 1 HETATM 19 O O3' SNI . . . E 2 4.561 19.039 -1.491 1 35.62 ? O3' SNI 746 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #