data_5DXB # _model_server_result.job_id aAoFAp7BwWWm2SNJeZQYVA _model_server_result.datetime_utc '2024-11-28 19:24:46' _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 5dxb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":603}' # _entry.id 5DXB # _exptl.entry_id 5DXB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 108.41 _cell.angle_gamma 90 _cell.entry_id 5DXB _cell.length_a 56.013 _cell.length_b 85.939 _cell.length_c 58.272 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DXB _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,D,F,G,H,I,K 1 1 A,C,E,J,L 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' 1_556 x,y,z+1 1 0 0 0 1 0 0 0 1 -18.403151 0 55.289692 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 G N N ? 5 H N 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 C LYS 236 A LYS 529 1_555 A N SCH 237 A SCH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.315 ? covale ? covale2 A C SCH 237 A SCH 530 1_555 A N LYS 238 A LYS 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale3 C C ACE 1 D ACE 1 1_555 C N HIS 2 D HIS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale4 C C LYS 3 D LYS 3 1_555 C N MK8 4 D MK8 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? covale ? covale5 C C MK8 4 D MK8 4 1_555 C N LEU 5 D LEU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale6 C CE MK8 4 D MK8 4 1_555 C CE 66D 8 D 66D 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.382 doub covale ? covale7 C C ARG 7 D ARG 7 1_555 C N 66D 8 D 66D 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? covale ? covale8 C C 66D 8 D 66D 8 1_555 C N LEU 9 D LEU 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale9 C C SER 12 D SER 12 1_555 C N NH2 13 D NH2 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.303 ? covale ? covale10 D C LYS 3 E LYS 3 1_555 D N MK8 4 E MK8 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? covale ? covale11 D C MK8 4 E MK8 4 1_555 D N LEU 5 E LEU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale12 D CE MK8 4 E MK8 4 1_555 D CE 66D 8 E 66D 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 doub covale ? covale13 D C ARG 7 E ARG 7 1_555 D N 66D 8 E 66D 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale14 D C 66D 8 E 66D 8 1_555 D N LEU 9 E LEU 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # _atom_sites.entry_id 5DXB _atom_sites.fract_transf_matrix[1][1] 0.017853 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005943 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011636 _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] 0.018087 _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 E 4 EST A 1 1000 1000 EST EST . F 4 EST B 1 601 601 EST EST . G 5 GOL B 1 602 602 GOL GOL . H 5 GOL B 1 603 603 GOL GOL . I 6 CL B 1 604 604 CL CL . J 7 HOH A 1 1101 1101 HOH HOH . J 7 HOH A 2 1102 1102 HOH HOH . J 7 HOH A 3 1103 1103 HOH HOH . J 7 HOH A 4 1104 1104 HOH HOH . J 7 HOH A 5 1105 1105 HOH HOH . J 7 HOH A 6 1106 1106 HOH HOH . J 7 HOH A 7 1107 1107 HOH HOH . J 7 HOH A 8 1108 1108 HOH HOH . J 7 HOH A 9 1109 1109 HOH HOH . J 7 HOH A 10 1110 1110 HOH HOH . J 7 HOH A 11 1111 1111 HOH HOH . J 7 HOH A 12 1112 1112 HOH HOH . J 7 HOH A 13 1113 1113 HOH HOH . J 7 HOH A 14 1114 1114 HOH HOH . J 7 HOH A 15 1115 1115 HOH HOH . J 7 HOH A 16 1116 1116 HOH HOH . J 7 HOH A 17 1117 1117 HOH HOH . J 7 HOH A 18 1118 1118 HOH HOH . J 7 HOH A 19 1119 1119 HOH HOH . J 7 HOH A 20 1120 1120 HOH HOH . J 7 HOH A 21 1121 1121 HOH HOH . J 7 HOH A 22 1122 1122 HOH HOH . J 7 HOH A 23 1123 1123 HOH HOH . J 7 HOH A 24 1124 1124 HOH HOH . J 7 HOH A 25 1125 1125 HOH HOH . J 7 HOH A 26 1126 1126 HOH HOH . J 7 HOH A 27 1127 1127 HOH HOH . J 7 HOH A 28 1128 1128 HOH HOH . J 7 HOH A 29 1129 1129 HOH HOH . J 7 HOH A 30 1130 1130 HOH HOH . J 7 HOH A 31 1131 1131 HOH HOH . J 7 HOH A 32 1132 1132 HOH HOH . J 7 HOH A 33 1133 1133 HOH HOH . J 7 HOH A 34 1134 1134 HOH HOH . J 7 HOH A 35 1135 1135 HOH HOH . J 7 HOH A 36 1136 1136 HOH HOH . J 7 HOH A 37 1137 1137 HOH HOH . J 7 HOH A 38 1138 1138 HOH HOH . J 7 HOH A 39 1139 1139 HOH HOH . J 7 HOH A 40 1140 1140 HOH HOH . J 7 HOH A 41 1141 1141 HOH HOH . J 7 HOH A 42 1142 1142 HOH HOH . J 7 HOH A 43 1143 1143 HOH HOH . J 7 HOH A 44 1144 1144 HOH HOH . J 7 HOH A 45 1145 1145 HOH HOH . J 7 HOH A 46 1146 1146 HOH HOH . J 7 HOH A 47 1147 1147 HOH HOH . J 7 HOH A 48 1148 1148 HOH HOH . J 7 HOH A 49 1149 1149 HOH HOH . J 7 HOH A 50 1150 1150 HOH HOH . J 7 HOH A 51 1151 1151 HOH HOH . J 7 HOH A 52 1152 1153 HOH HOH . J 7 HOH A 53 1153 1154 HOH HOH . J 7 HOH A 54 1154 1155 HOH HOH . J 7 HOH A 55 1155 1156 HOH HOH . J 7 HOH A 56 1156 1157 HOH HOH . J 7 HOH A 57 1157 1158 HOH HOH . J 7 HOH A 58 1158 1159 HOH HOH . J 7 HOH A 59 1159 1160 HOH HOH . J 7 HOH A 60 1160 1152 HOH HOH . J 7 HOH A 61 1161 1161 HOH HOH . J 7 HOH A 62 1162 1162 HOH HOH . J 7 HOH A 63 1163 1163 HOH HOH . J 7 HOH A 64 1164 1164 HOH HOH . J 7 HOH A 65 1165 1165 HOH HOH . J 7 HOH A 66 1166 1166 HOH HOH . J 7 HOH A 67 1167 1167 HOH HOH . J 7 HOH A 68 1168 1168 HOH HOH . J 7 HOH A 69 1169 1169 HOH HOH . J 7 HOH A 70 1170 1170 HOH HOH . J 7 HOH A 71 1171 1171 HOH HOH . J 7 HOH A 72 1172 1172 HOH HOH . J 7 HOH A 73 1173 1173 HOH HOH . J 7 HOH A 74 1174 1174 HOH HOH . J 7 HOH A 75 1175 1175 HOH HOH . J 7 HOH A 76 1176 1176 HOH HOH . J 7 HOH A 77 1177 1177 HOH HOH . J 7 HOH A 78 1178 1178 HOH HOH . J 7 HOH A 79 1179 1179 HOH HOH . J 7 HOH A 80 1180 1180 HOH HOH . J 7 HOH A 81 1181 1181 HOH HOH . J 7 HOH A 82 1182 1182 HOH HOH . J 7 HOH A 83 1183 1183 HOH HOH . J 7 HOH A 84 1184 1184 HOH HOH . J 7 HOH A 85 1185 1185 HOH HOH . J 7 HOH A 86 1186 1186 HOH HOH . J 7 HOH A 87 1187 1187 HOH HOH . J 7 HOH A 88 1188 1188 HOH HOH . J 7 HOH A 89 1189 1189 HOH HOH . J 7 HOH A 90 1190 1190 HOH HOH . J 7 HOH A 91 1191 1191 HOH HOH . J 7 HOH A 92 1192 1192 HOH HOH . J 7 HOH A 93 1193 1193 HOH HOH . J 7 HOH A 94 1194 1194 HOH HOH . J 7 HOH A 95 1195 1195 HOH HOH . J 7 HOH A 96 1196 1196 HOH HOH . J 7 HOH A 97 1197 1197 HOH HOH . J 7 HOH A 98 1198 1198 HOH HOH . J 7 HOH A 99 1199 1199 HOH HOH . K 7 HOH B 1 701 701 HOH HOH . K 7 HOH B 2 702 702 HOH HOH . K 7 HOH B 3 703 703 HOH HOH . K 7 HOH B 4 704 704 HOH HOH . K 7 HOH B 5 705 705 HOH HOH . K 7 HOH B 6 706 706 HOH HOH . K 7 HOH B 7 707 707 HOH HOH . K 7 HOH B 8 708 708 HOH HOH . K 7 HOH B 9 709 709 HOH HOH . K 7 HOH B 10 710 710 HOH HOH . K 7 HOH B 11 711 711 HOH HOH . K 7 HOH B 12 712 712 HOH HOH . K 7 HOH B 13 713 713 HOH HOH . K 7 HOH B 14 714 714 HOH HOH . K 7 HOH B 15 715 715 HOH HOH . K 7 HOH B 16 716 716 HOH HOH . K 7 HOH B 17 717 717 HOH HOH . K 7 HOH B 18 718 718 HOH HOH . K 7 HOH B 19 719 719 HOH HOH . K 7 HOH B 20 720 720 HOH HOH . K 7 HOH B 21 721 721 HOH HOH . K 7 HOH B 22 722 722 HOH HOH . K 7 HOH B 23 723 723 HOH HOH . K 7 HOH B 24 724 724 HOH HOH . K 7 HOH B 25 725 725 HOH HOH . K 7 HOH B 26 726 726 HOH HOH . K 7 HOH B 27 727 727 HOH HOH . K 7 HOH B 28 728 728 HOH HOH . K 7 HOH B 29 729 729 HOH HOH . K 7 HOH B 30 730 730 HOH HOH . K 7 HOH B 31 731 731 HOH HOH . K 7 HOH B 32 732 732 HOH HOH . K 7 HOH B 33 733 733 HOH HOH . K 7 HOH B 34 734 734 HOH HOH . K 7 HOH B 35 735 735 HOH HOH . K 7 HOH B 36 736 736 HOH HOH . K 7 HOH B 37 737 737 HOH HOH . K 7 HOH B 38 738 738 HOH HOH . K 7 HOH B 39 739 739 HOH HOH . K 7 HOH B 40 740 740 HOH HOH . K 7 HOH B 41 741 741 HOH HOH . K 7 HOH B 42 742 742 HOH HOH . K 7 HOH B 43 743 743 HOH HOH . K 7 HOH B 44 744 744 HOH HOH . K 7 HOH B 45 745 745 HOH HOH . K 7 HOH B 46 746 746 HOH HOH . K 7 HOH B 47 747 747 HOH HOH . K 7 HOH B 48 748 748 HOH HOH . K 7 HOH B 49 749 749 HOH HOH . K 7 HOH B 50 750 750 HOH HOH . K 7 HOH B 51 751 751 HOH HOH . K 7 HOH B 52 752 752 HOH HOH . K 7 HOH B 53 753 753 HOH HOH . K 7 HOH B 54 754 754 HOH HOH . K 7 HOH B 55 755 755 HOH HOH . K 7 HOH B 56 756 756 HOH HOH . K 7 HOH B 57 757 757 HOH HOH . K 7 HOH B 58 758 758 HOH HOH . K 7 HOH B 59 759 759 HOH HOH . K 7 HOH B 60 760 760 HOH HOH . K 7 HOH B 61 761 761 HOH HOH . K 7 HOH B 62 762 762 HOH HOH . K 7 HOH B 63 763 763 HOH HOH . L 7 HOH D 1 101 101 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 GOL . . . H 5 -9.495 7.651 20.815 1 45.24 ? C1 GOL 603 B 1 HETATM 2 O O1 GOL . . . H 5 -10.155 6.411 20.921 1 45.85 ? O1 GOL 603 B 1 HETATM 3 C C2 GOL . . . H 5 -10.001 8.458 21.992 1 45.13 ? C2 GOL 603 B 1 HETATM 4 O O2 GOL . . . H 5 -10.344 7.492 22.96 1 46.11 ? O2 GOL 603 B 1 HETATM 5 C C3 GOL . . . H 5 -8.948 9.428 22.524 1 44.24 ? C3 GOL 603 B 1 HETATM 6 O O3 GOL . . . H 5 -8.611 10.377 21.535 1 44.24 ? O3 GOL 603 B 1 HETATM 7 H H11 GOL . . . H 5 -8.415 7.519 20.874 1 54.29 ? H11 GOL 603 B 1 HETATM 8 H H12 GOL . . . H 5 -9.745 8.142 19.875 1 54.29 ? H12 GOL 603 B 1 HETATM 9 H HO1 GOL . . . H 5 -9.925 5.853 20.149 1 55.02 ? HO1 GOL 603 B 1 HETATM 10 H H2 GOL . . . H 5 -10.885 9.019 21.687 1 54.16 ? H2 GOL 603 B 1 HETATM 11 H HO2 GOL . . . H 5 -9.544 6.988 23.217 1 55.33 ? HO2 GOL 603 B 1 HETATM 12 H H31 GOL . . . H 5 -9.335 9.939 23.405 1 53.09 ? H31 GOL 603 B 1 HETATM 13 H H32 GOL . . . H 5 -8.057 8.874 22.818 1 53.09 ? H32 GOL 603 B 1 HETATM 14 H HO3 GOL . . . H 5 -8.718 9.976 20.647 1 53.09 ? HO3 GOL 603 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 494 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #