data_5L9Y # _model_server_result.job_id s0xKjp8JTIOdfgVtBzoeVA _model_server_result.datetime_utc '2024-10-14 21:25:39' _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 5l9y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":607}' # _entry.id 5L9Y # _exptl.entry_id 5L9Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _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 94.92 _cell.angle_gamma 90 _cell.entry_id 5L9Y _cell.length_a 46.43 _cell.length_b 71.26 _cell.length_c 78.91 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L9Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,J,K _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 G N N ? 5 H N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 FUC _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O6 _pdbx_entity_branch_link.leaving_atom_id_2 HO6 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG F 5 NAG 3 n C FUC 2 C 2 FUC F 6 FUC # 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 disulf ? disulf1 A SG CYS 283 A CYS 437 1_555 A SG CYS 388 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 46 A ASN 200 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 84 A ASN 238 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 A OE2 GLU 189 A GLU 343 1_555 I C1 6S6 . A 6S6 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 305 A ASN 459 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? # _chem_comp.formula 'C2 H6 O2' _chem_comp.formula_weight 62.068 _chem_comp.id EDO _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-ETHANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ETHYLENE GLYCOL' # 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 C1 O1 EDO sing 136 n n C1 C2 EDO sing 137 n n C1 H11 EDO sing 138 n n C1 H12 EDO sing 139 n n O1 HO1 EDO sing 140 n n C2 O2 EDO sing 141 n n C2 H21 EDO sing 142 n n C2 H22 EDO sing 143 n n O2 HO2 EDO sing 144 n n # _atom_sites.entry_id 5L9Y _atom_sites.fract_transf_matrix[1][1] 0.021538 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001854 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014033 _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] 0.01272 _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 4 NAG A 1 601 2 NAG NAG . E 4 NAG A 1 602 4 NAG NAG . F 5 EDO A 1 605 1 EDO EDO . G 5 EDO A 1 606 2 EDO EDO . H 5 EDO A 1 607 3 EDO EDO . I 6 6S6 A 1 608 1 6S6 355 . J 7 HOH A 1 701 38 HOH HOH . J 7 HOH A 2 702 286 HOH HOH . J 7 HOH A 3 703 63 HOH HOH . J 7 HOH A 4 704 103 HOH HOH . J 7 HOH A 5 705 171 HOH HOH . J 7 HOH A 6 706 74 HOH HOH . J 7 HOH A 7 707 54 HOH HOH . J 7 HOH A 8 708 254 HOH HOH . J 7 HOH A 9 709 49 HOH HOH . J 7 HOH A 10 710 59 HOH HOH . J 7 HOH A 11 711 174 HOH HOH . J 7 HOH A 12 712 162 HOH HOH . J 7 HOH A 13 713 250 HOH HOH . J 7 HOH A 14 714 289 HOH HOH . J 7 HOH A 15 715 184 HOH HOH . J 7 HOH A 16 716 295 HOH HOH . J 7 HOH A 17 717 69 HOH HOH . J 7 HOH A 18 718 204 HOH HOH . J 7 HOH A 19 719 19 HOH HOH . J 7 HOH A 20 720 120 HOH HOH . J 7 HOH A 21 721 293 HOH HOH . J 7 HOH A 22 722 68 HOH HOH . J 7 HOH A 23 723 24 HOH HOH . J 7 HOH A 24 724 56 HOH HOH . J 7 HOH A 25 725 146 HOH HOH . J 7 HOH A 26 726 164 HOH HOH . J 7 HOH A 27 727 177 HOH HOH . J 7 HOH A 28 728 215 HOH HOH . J 7 HOH A 29 729 288 HOH HOH . J 7 HOH A 30 730 9 HOH HOH . J 7 HOH A 31 731 131 HOH HOH . J 7 HOH A 32 732 107 HOH HOH . J 7 HOH A 33 733 262 HOH HOH . J 7 HOH A 34 734 200 HOH HOH . J 7 HOH A 35 735 36 HOH HOH . J 7 HOH A 36 736 248 HOH HOH . J 7 HOH A 37 737 148 HOH HOH . J 7 HOH A 38 738 86 HOH HOH . J 7 HOH A 39 739 78 HOH HOH . J 7 HOH A 40 740 7 HOH HOH . J 7 HOH A 41 741 117 HOH HOH . J 7 HOH A 42 742 40 HOH HOH . J 7 HOH A 43 743 264 HOH HOH . J 7 HOH A 44 744 282 HOH HOH . J 7 HOH A 45 745 53 HOH HOH . J 7 HOH A 46 746 28 HOH HOH . J 7 HOH A 47 747 25 HOH HOH . J 7 HOH A 48 748 71 HOH HOH . J 7 HOH A 49 749 269 HOH HOH . J 7 HOH A 50 750 205 HOH HOH . J 7 HOH A 51 751 151 HOH HOH . J 7 HOH A 52 752 198 HOH HOH . J 7 HOH A 53 753 238 HOH HOH . J 7 HOH A 54 754 203 HOH HOH . J 7 HOH A 55 755 222 HOH HOH . J 7 HOH A 56 756 41 HOH HOH . J 7 HOH A 57 757 135 HOH HOH . J 7 HOH A 58 758 130 HOH HOH . J 7 HOH A 59 759 16 HOH HOH . J 7 HOH A 60 760 173 HOH HOH . J 7 HOH A 61 761 11 HOH HOH . J 7 HOH A 62 762 23 HOH HOH . J 7 HOH A 63 763 224 HOH HOH . J 7 HOH A 64 764 126 HOH HOH . J 7 HOH A 65 765 73 HOH HOH . J 7 HOH A 66 766 155 HOH HOH . J 7 HOH A 67 767 190 HOH HOH . J 7 HOH A 68 768 142 HOH HOH . J 7 HOH A 69 769 61 HOH HOH . J 7 HOH A 70 770 87 HOH HOH . J 7 HOH A 71 771 255 HOH HOH . J 7 HOH A 72 772 197 HOH HOH . J 7 HOH A 73 773 272 HOH HOH . J 7 HOH A 74 774 113 HOH HOH . J 7 HOH A 75 775 182 HOH HOH . J 7 HOH A 76 776 246 HOH HOH . J 7 HOH A 77 777 267 HOH HOH . J 7 HOH A 78 778 20 HOH HOH . J 7 HOH A 79 779 76 HOH HOH . J 7 HOH A 80 780 51 HOH HOH . J 7 HOH A 81 781 14 HOH HOH . J 7 HOH A 82 782 30 HOH HOH . J 7 HOH A 83 783 144 HOH HOH . J 7 HOH A 84 784 95 HOH HOH . J 7 HOH A 85 785 279 HOH HOH . J 7 HOH A 86 786 220 HOH HOH . J 7 HOH A 87 787 4 HOH HOH . J 7 HOH A 88 788 187 HOH HOH . J 7 HOH A 89 789 99 HOH HOH . J 7 HOH A 90 790 17 HOH HOH . J 7 HOH A 91 791 6 HOH HOH . J 7 HOH A 92 792 15 HOH HOH . J 7 HOH A 93 793 94 HOH HOH . J 7 HOH A 94 794 278 HOH HOH . J 7 HOH A 95 795 44 HOH HOH . J 7 HOH A 96 796 128 HOH HOH . J 7 HOH A 97 797 206 HOH HOH . J 7 HOH A 98 798 211 HOH HOH . J 7 HOH A 99 799 88 HOH HOH . J 7 HOH A 100 800 83 HOH HOH . J 7 HOH A 101 801 35 HOH HOH . J 7 HOH A 102 802 236 HOH HOH . J 7 HOH A 103 803 108 HOH HOH . J 7 HOH A 104 804 273 HOH HOH . J 7 HOH A 105 805 195 HOH HOH . J 7 HOH A 106 806 27 HOH HOH . J 7 HOH A 107 807 284 HOH HOH . J 7 HOH A 108 808 84 HOH HOH . J 7 HOH A 109 809 13 HOH HOH . J 7 HOH A 110 810 183 HOH HOH . J 7 HOH A 111 811 65 HOH HOH . J 7 HOH A 112 812 237 HOH HOH . J 7 HOH A 113 813 39 HOH HOH . J 7 HOH A 114 814 239 HOH HOH . J 7 HOH A 115 815 45 HOH HOH . J 7 HOH A 116 816 43 HOH HOH . J 7 HOH A 117 817 55 HOH HOH . J 7 HOH A 118 818 217 HOH HOH . J 7 HOH A 119 819 175 HOH HOH . J 7 HOH A 120 820 92 HOH HOH . J 7 HOH A 121 821 46 HOH HOH . J 7 HOH A 122 822 72 HOH HOH . J 7 HOH A 123 823 225 HOH HOH . J 7 HOH A 124 824 266 HOH HOH . J 7 HOH A 125 825 64 HOH HOH . J 7 HOH A 126 826 47 HOH HOH . J 7 HOH A 127 827 34 HOH HOH . J 7 HOH A 128 828 2 HOH HOH . J 7 HOH A 129 829 37 HOH HOH . J 7 HOH A 130 830 233 HOH HOH . J 7 HOH A 131 831 118 HOH HOH . J 7 HOH A 132 832 140 HOH HOH . J 7 HOH A 133 833 169 HOH HOH . J 7 HOH A 134 834 121 HOH HOH . J 7 HOH A 135 835 22 HOH HOH . J 7 HOH A 136 836 5 HOH HOH . J 7 HOH A 137 837 114 HOH HOH . J 7 HOH A 138 838 62 HOH HOH . J 7 HOH A 139 839 168 HOH HOH . J 7 HOH A 140 840 18 HOH HOH . J 7 HOH A 141 841 134 HOH HOH . J 7 HOH A 142 842 159 HOH HOH . J 7 HOH A 143 843 48 HOH HOH . J 7 HOH A 144 844 216 HOH HOH . J 7 HOH A 145 845 207 HOH HOH . J 7 HOH A 146 846 153 HOH HOH . J 7 HOH A 147 847 257 HOH HOH . J 7 HOH A 148 848 244 HOH HOH . J 7 HOH A 149 849 10 HOH HOH . J 7 HOH A 150 850 209 HOH HOH . J 7 HOH A 151 851 77 HOH HOH . J 7 HOH A 152 852 234 HOH HOH . J 7 HOH A 153 853 280 HOH HOH . J 7 HOH A 154 854 229 HOH HOH . J 7 HOH A 155 855 158 HOH HOH . J 7 HOH A 156 856 79 HOH HOH . J 7 HOH A 157 857 12 HOH HOH . J 7 HOH A 158 858 189 HOH HOH . J 7 HOH A 159 859 219 HOH HOH . J 7 HOH A 160 860 26 HOH HOH . J 7 HOH A 161 861 172 HOH HOH . J 7 HOH A 162 862 139 HOH HOH . J 7 HOH A 163 863 268 HOH HOH . J 7 HOH A 164 864 31 HOH HOH . J 7 HOH A 165 865 137 HOH HOH . J 7 HOH A 166 866 152 HOH HOH . J 7 HOH A 167 867 259 HOH HOH . J 7 HOH A 168 868 52 HOH HOH . J 7 HOH A 169 869 21 HOH HOH . J 7 HOH A 170 870 180 HOH HOH . J 7 HOH A 171 871 176 HOH HOH . J 7 HOH A 172 872 249 HOH HOH . J 7 HOH A 173 873 127 HOH HOH . J 7 HOH A 174 874 149 HOH HOH . J 7 HOH A 175 875 136 HOH HOH . J 7 HOH A 176 876 170 HOH HOH . J 7 HOH A 177 877 252 HOH HOH . J 7 HOH A 178 878 208 HOH HOH . J 7 HOH A 179 879 218 HOH HOH . J 7 HOH A 180 880 241 HOH HOH . J 7 HOH A 181 881 226 HOH HOH . J 7 HOH A 182 882 178 HOH HOH . J 7 HOH A 183 883 166 HOH HOH . J 7 HOH A 184 884 129 HOH HOH . J 7 HOH A 185 885 242 HOH HOH . J 7 HOH A 186 886 247 HOH HOH . J 7 HOH A 187 887 191 HOH HOH . J 7 HOH A 188 888 221 HOH HOH . J 7 HOH A 189 889 243 HOH HOH . J 7 HOH A 190 890 199 HOH HOH . J 7 HOH A 191 891 156 HOH HOH . J 7 HOH A 192 892 70 HOH HOH . J 7 HOH A 193 893 186 HOH HOH . J 7 HOH A 194 894 181 HOH HOH . J 7 HOH A 195 895 210 HOH HOH . J 7 HOH A 196 896 185 HOH HOH . J 7 HOH A 197 897 212 HOH HOH . J 7 HOH A 198 898 245 HOH HOH . J 7 HOH A 199 899 230 HOH HOH . K 7 HOH B 1 201 132 HOH HOH . K 7 HOH B 2 202 42 HOH HOH . K 7 HOH B 3 203 97 HOH HOH . K 7 HOH B 4 204 57 HOH HOH . K 7 HOH B 5 205 193 HOH HOH . K 7 HOH B 6 206 50 HOH HOH . K 7 HOH B 7 207 89 HOH HOH . K 7 HOH B 8 208 143 HOH HOH . K 7 HOH B 9 209 67 HOH HOH . K 7 HOH B 10 210 228 HOH HOH . K 7 HOH B 11 211 82 HOH HOH . K 7 HOH B 12 212 96 HOH HOH . K 7 HOH B 13 213 138 HOH HOH . K 7 HOH B 14 214 106 HOH HOH . K 7 HOH B 15 215 115 HOH HOH . K 7 HOH B 16 216 33 HOH HOH . K 7 HOH B 17 217 75 HOH HOH . K 7 HOH B 18 218 100 HOH HOH . K 7 HOH B 19 219 90 HOH HOH . K 7 HOH B 20 220 123 HOH HOH . K 7 HOH B 21 221 98 HOH HOH . K 7 HOH B 22 222 227 HOH HOH . K 7 HOH B 23 223 165 HOH HOH . K 7 HOH B 24 224 32 HOH HOH . K 7 HOH B 25 225 167 HOH HOH . K 7 HOH B 26 226 192 HOH HOH . K 7 HOH B 27 227 251 HOH HOH . K 7 HOH B 28 228 145 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 C1 EDO . . . H 5 0.233 20.094 28.333 1 54.92 ? C1 EDO 607 A 1 HETATM 2 O O1 EDO . . . H 5 0.708 20.157 29.671 1 58.57 ? O1 EDO 607 A 1 HETATM 3 C C2 EDO . . . H 5 0.909 18.893 27.69 1 55.21 ? C2 EDO 607 A 1 HETATM 4 O O2 EDO . . . H 5 2.355 18.978 27.719 1 53.82 ? O2 EDO 607 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 64 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 4 #