data_5JP1 # _model_server_result.job_id Q2gA21XRapHtO5E_Phm_ug _model_server_result.datetime_utc '2024-11-05 01:01:51' _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 5jp1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 5JP1 # _exptl.entry_id 5JP1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 152.235 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S,5S)-1,2-DITHIANE-4,5-DIOL _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 5JP1 _cell.length_a 119.103 _cell.length_b 119.103 _cell.length_c 50.463 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JP1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 4 _struct_asym.id D _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 covale ? covale1 A SG CYS 175 A CYS 470 1_555 B C2 AYE 96 B AYE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.66 ? covale ? covale2 B C GLY 95 B GLY 95 1_555 B N1 AYE 96 B AYE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? # _chem_comp.formula 'C4 H8 O2 S2' _chem_comp.formula_weight 152.235 _chem_comp.id D1D _chem_comp.mon_nstd_flag . _chem_comp.name (4S,5S)-1,2-DITHIANE-4,5-DIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 S1 C1 D1D sing 93 n n S1 S4 D1D sing 94 n n C1 C2 D1D sing 95 n n C1 H1C1 D1D sing 96 n n C1 H1C2 D1D sing 97 n n C2 O2 D1D sing 98 n n C2 C3 D1D sing 99 n n C2 H2 D1D sing 100 n n O2 HA D1D sing 101 n n C3 O3 D1D sing 102 n n C3 C4 D1D sing 103 n n C3 H3 D1D sing 104 n n O3 HB D1D sing 105 n n C4 S4 D1D sing 106 n n C4 H4C1 D1D sing 107 n n C4 H4C2 D1D sing 108 n n # _atom_sites.entry_id 5JP1 _atom_sites.fract_transf_matrix[1][1] 0.008396 _atom_sites.fract_transf_matrix[1][2] 0.004847 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009695 _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] 0.019816 _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 C 3 MLI A 1 601 2 MLI MLI . D 4 D1D A 1 602 1 D1D D1D . E 3 MLI B 1 101 1 MLI MLI . F 5 HOH A 1 701 175 HOH HOH . F 5 HOH A 2 702 103 HOH HOH . F 5 HOH A 3 703 214 HOH HOH . F 5 HOH A 4 704 44 HOH HOH . F 5 HOH A 5 705 39 HOH HOH . F 5 HOH A 6 706 42 HOH HOH . F 5 HOH A 7 707 131 HOH HOH . F 5 HOH A 8 708 81 HOH HOH . F 5 HOH A 9 709 230 HOH HOH . F 5 HOH A 10 710 86 HOH HOH . F 5 HOH A 11 711 58 HOH HOH . F 5 HOH A 12 712 207 HOH HOH . F 5 HOH A 13 713 104 HOH HOH . F 5 HOH A 14 714 78 HOH HOH . F 5 HOH A 15 715 173 HOH HOH . F 5 HOH A 16 716 99 HOH HOH . F 5 HOH A 17 717 102 HOH HOH . F 5 HOH A 18 718 226 HOH HOH . F 5 HOH A 19 719 142 HOH HOH . F 5 HOH A 20 720 74 HOH HOH . F 5 HOH A 21 721 12 HOH HOH . F 5 HOH A 22 722 38 HOH HOH . F 5 HOH A 23 723 32 HOH HOH . F 5 HOH A 24 724 70 HOH HOH . F 5 HOH A 25 725 16 HOH HOH . F 5 HOH A 26 726 5 HOH HOH . F 5 HOH A 27 727 17 HOH HOH . F 5 HOH A 28 728 29 HOH HOH . F 5 HOH A 29 729 236 HOH HOH . F 5 HOH A 30 730 60 HOH HOH . F 5 HOH A 31 731 52 HOH HOH . F 5 HOH A 32 732 34 HOH HOH . F 5 HOH A 33 733 210 HOH HOH . F 5 HOH A 34 734 30 HOH HOH . F 5 HOH A 35 735 221 HOH HOH . F 5 HOH A 36 736 152 HOH HOH . F 5 HOH A 37 737 119 HOH HOH . F 5 HOH A 38 738 35 HOH HOH . F 5 HOH A 39 739 120 HOH HOH . F 5 HOH A 40 740 113 HOH HOH . F 5 HOH A 41 741 4 HOH HOH . F 5 HOH A 42 742 46 HOH HOH . F 5 HOH A 43 743 205 HOH HOH . F 5 HOH A 44 744 101 HOH HOH . F 5 HOH A 45 745 228 HOH HOH . F 5 HOH A 46 746 211 HOH HOH . F 5 HOH A 47 747 222 HOH HOH . F 5 HOH A 48 748 229 HOH HOH . F 5 HOH A 49 749 37 HOH HOH . F 5 HOH A 50 750 21 HOH HOH . F 5 HOH A 51 751 25 HOH HOH . F 5 HOH A 52 752 87 HOH HOH . F 5 HOH A 53 753 223 HOH HOH . F 5 HOH A 54 754 231 HOH HOH . F 5 HOH A 55 755 31 HOH HOH . F 5 HOH A 56 756 83 HOH HOH . F 5 HOH A 57 757 66 HOH HOH . F 5 HOH A 58 758 168 HOH HOH . F 5 HOH A 59 759 130 HOH HOH . F 5 HOH A 60 760 220 HOH HOH . F 5 HOH A 61 761 117 HOH HOH . F 5 HOH A 62 762 27 HOH HOH . F 5 HOH A 63 763 203 HOH HOH . F 5 HOH A 64 764 106 HOH HOH . F 5 HOH A 65 765 91 HOH HOH . F 5 HOH A 66 766 65 HOH HOH . F 5 HOH A 67 767 140 HOH HOH . F 5 HOH A 68 768 94 HOH HOH . F 5 HOH A 69 769 1 HOH HOH . F 5 HOH A 70 770 187 HOH HOH . F 5 HOH A 71 771 149 HOH HOH . F 5 HOH A 72 772 57 HOH HOH . F 5 HOH A 73 773 72 HOH HOH . F 5 HOH A 74 774 89 HOH HOH . F 5 HOH A 75 775 77 HOH HOH . F 5 HOH A 76 776 114 HOH HOH . F 5 HOH A 77 777 235 HOH HOH . F 5 HOH A 78 778 3 HOH HOH . F 5 HOH A 79 779 198 HOH HOH . F 5 HOH A 80 780 129 HOH HOH . F 5 HOH A 81 781 202 HOH HOH . F 5 HOH A 82 782 174 HOH HOH . F 5 HOH A 83 783 15 HOH HOH . F 5 HOH A 84 784 80 HOH HOH . F 5 HOH A 85 785 59 HOH HOH . F 5 HOH A 86 786 112 HOH HOH . F 5 HOH A 87 787 154 HOH HOH . F 5 HOH A 88 788 20 HOH HOH . F 5 HOH A 89 789 150 HOH HOH . F 5 HOH A 90 790 171 HOH HOH . F 5 HOH A 91 791 2 HOH HOH . F 5 HOH A 92 792 155 HOH HOH . F 5 HOH A 93 793 7 HOH HOH . F 5 HOH A 94 794 96 HOH HOH . F 5 HOH A 95 795 151 HOH HOH . F 5 HOH A 96 796 206 HOH HOH . F 5 HOH A 97 797 128 HOH HOH . F 5 HOH A 98 798 68 HOH HOH . F 5 HOH A 99 799 85 HOH HOH . F 5 HOH A 100 800 159 HOH HOH . F 5 HOH A 101 801 208 HOH HOH . F 5 HOH A 102 802 55 HOH HOH . F 5 HOH A 103 803 121 HOH HOH . F 5 HOH A 104 804 144 HOH HOH . F 5 HOH A 105 805 197 HOH HOH . F 5 HOH A 106 806 97 HOH HOH . F 5 HOH A 107 807 196 HOH HOH . F 5 HOH A 108 808 160 HOH HOH . F 5 HOH A 109 809 111 HOH HOH . F 5 HOH A 110 810 105 HOH HOH . F 5 HOH A 111 811 122 HOH HOH . F 5 HOH A 112 812 108 HOH HOH . F 5 HOH A 113 813 195 HOH HOH . F 5 HOH A 114 814 107 HOH HOH . F 5 HOH A 115 815 82 HOH HOH . F 5 HOH A 116 816 212 HOH HOH . F 5 HOH A 117 817 18 HOH HOH . F 5 HOH A 118 818 24 HOH HOH . F 5 HOH A 119 819 127 HOH HOH . F 5 HOH A 120 820 213 HOH HOH . F 5 HOH A 121 821 93 HOH HOH . F 5 HOH A 122 822 193 HOH HOH . F 5 HOH A 123 823 157 HOH HOH . F 5 HOH A 124 824 134 HOH HOH . F 5 HOH A 125 825 153 HOH HOH . F 5 HOH A 126 826 176 HOH HOH . F 5 HOH A 127 827 165 HOH HOH . F 5 HOH A 128 828 115 HOH HOH . F 5 HOH A 129 829 237 HOH HOH . F 5 HOH A 130 830 232 HOH HOH . F 5 HOH A 131 831 217 HOH HOH . F 5 HOH A 132 832 209 HOH HOH . F 5 HOH A 133 833 147 HOH HOH . F 5 HOH A 134 834 192 HOH HOH . F 5 HOH A 135 835 148 HOH HOH . F 5 HOH A 136 836 200 HOH HOH . F 5 HOH A 137 837 201 HOH HOH . F 5 HOH A 138 838 172 HOH HOH . F 5 HOH A 139 839 215 HOH HOH . F 5 HOH A 140 840 199 HOH HOH . F 5 HOH A 141 841 169 HOH HOH . F 5 HOH A 142 842 90 HOH HOH . F 5 HOH A 143 843 238 HOH HOH . F 5 HOH A 144 844 146 HOH HOH . F 5 HOH A 145 845 224 HOH HOH . F 5 HOH A 146 846 194 HOH HOH . F 5 HOH A 147 847 239 HOH HOH . F 5 HOH A 148 848 225 HOH HOH . G 5 HOH B 1 201 216 HOH HOH . G 5 HOH B 2 202 137 HOH HOH . G 5 HOH B 3 203 61 HOH HOH . G 5 HOH B 4 204 76 HOH HOH . G 5 HOH B 5 205 180 HOH HOH . G 5 HOH B 6 206 139 HOH HOH . G 5 HOH B 7 207 125 HOH HOH . G 5 HOH B 8 208 185 HOH HOH . G 5 HOH B 9 209 8 HOH HOH . G 5 HOH B 10 210 51 HOH HOH . G 5 HOH B 11 211 48 HOH HOH . G 5 HOH B 12 212 50 HOH HOH . G 5 HOH B 13 213 135 HOH HOH . G 5 HOH B 14 214 47 HOH HOH . G 5 HOH B 15 215 19 HOH HOH . G 5 HOH B 16 216 141 HOH HOH . G 5 HOH B 17 217 162 HOH HOH . G 5 HOH B 18 218 177 HOH HOH . G 5 HOH B 19 219 56 HOH HOH . G 5 HOH B 20 220 13 HOH HOH . G 5 HOH B 21 221 26 HOH HOH . G 5 HOH B 22 222 36 HOH HOH . G 5 HOH B 23 223 166 HOH HOH . G 5 HOH B 24 224 54 HOH HOH . G 5 HOH B 25 225 204 HOH HOH . G 5 HOH B 26 226 164 HOH HOH . G 5 HOH B 27 227 143 HOH HOH . G 5 HOH B 28 228 183 HOH HOH . G 5 HOH B 29 229 62 HOH HOH . G 5 HOH B 30 230 124 HOH HOH . G 5 HOH B 31 231 133 HOH HOH . G 5 HOH B 32 232 182 HOH HOH . G 5 HOH B 33 233 100 HOH HOH . G 5 HOH B 34 234 181 HOH HOH . G 5 HOH B 35 235 161 HOH HOH . G 5 HOH B 36 236 138 HOH HOH . G 5 HOH B 37 237 23 HOH HOH . G 5 HOH B 38 238 132 HOH HOH . G 5 HOH B 39 239 145 HOH HOH . G 5 HOH B 40 240 158 HOH HOH . G 5 HOH B 41 241 186 HOH HOH . G 5 HOH B 42 242 179 HOH HOH . G 5 HOH B 43 243 136 HOH HOH . G 5 HOH B 44 244 191 HOH HOH . G 5 HOH B 45 245 178 HOH HOH . G 5 HOH B 46 246 188 HOH HOH . G 5 HOH B 47 247 123 HOH HOH . G 5 HOH B 48 248 163 HOH HOH . G 5 HOH B 49 249 126 HOH HOH . G 5 HOH B 50 250 227 HOH HOH . G 5 HOH B 51 251 184 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 S S1 D1D . . . D 4 59.933 0.351 -13.569 0.5 67.71 ? S1 D1D 602 A 1 HETATM 2 C C1 D1D . . . D 4 60.963 0.541 -14.836 0.5 66.46 ? C1 D1D 602 A 1 HETATM 3 C C2 D1D . . . D 4 60.205 0.674 -16.282 0.5 65.31 ? C2 D1D 602 A 1 HETATM 4 O O2 D1D . . . D 4 61.046 0.498 -17.174 0.5 65.01 ? O2 D1D 602 A 1 HETATM 5 C C3 D1D . . . D 4 58.896 -0.465 -16.536 0.5 65.39 ? C3 D1D 602 A 1 HETATM 6 O O3 D1D . . . D 4 58.165 -0.015 -17.429 0.5 64.93 ? O3 D1D 602 A 1 HETATM 7 C C4 D1D . . . D 4 57.969 -0.755 -15.218 0.5 65.88 ? C4 D1D 602 A 1 HETATM 8 S S4 D1D . . . D 4 58.849 -1.002 -13.852 0.5 67.47 ? S4 D1D 602 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #