data_6DZY # _model_server_result.job_id lK1bhbBPqBLbkwWPQ73rQQ _model_server_result.datetime_utc '2025-01-05 05:27:20' _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 6dzy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":701}' # _entry.id 6DZY # _exptl.entry_id 6DZY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 310.433 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5beta)-12-methoxyibogamine _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 90 _cell.entry_id 6DZY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DZY _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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 ? _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 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 5 _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 NAG _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 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _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 5 n E NAG 1 B 1 NAG A 703 NAG 5 n E NAG 2 B 2 NAG A 704 NAG # 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 122 A CYS 200 1_555 A SG CYS 131 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 B SG CYS 22 H CYS 41 1_555 B SG CYS 96 H CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 C SG CYS 23 L CYS 43 1_555 C SG CYS 92 L CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 D SG CYS 22 V CYS 37 1_555 D SG CYS 96 V CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 D SG CYS 157 V CYS 172 1_555 D SG CYS 222 V CYS 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 E O4 NAG . B NAG 1 1_555 E C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _chem_comp.formula 'C20 H26 N2 O' _chem_comp.formula_weight 310.433 _chem_comp.id HJM _chem_comp.mon_nstd_flag . _chem_comp.name (5beta)-12-methoxyibogamine _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 C20 O HJM sing 150 n n O C18 HJM sing 151 n n C18 C16 HJM doub 152 n y C18 C19 HJM sing 153 n y C16 C13 HJM sing 154 n y C19 C17 HJM doub 155 n y C12 C9 HJM sing 156 n n C12 C11 HJM sing 157 n n C13 C11 HJM sing 158 n y C13 C15 HJM doub 159 n y C9 N1 HJM sing 160 n n C17 C15 HJM sing 161 n y C11 C8 HJM doub 162 n y C15 N2 HJM sing 163 n y N1 C7 HJM sing 164 n n N1 C1 HJM sing 165 n n C8 N2 HJM sing 166 n y C8 C2 HJM sing 167 n n C7 C3 HJM sing 168 n n C1 C2 HJM sing 169 n n C1 C4 HJM sing 170 n n C2 C5 HJM sing 171 n n C5 C3 HJM sing 172 n n C3 C6 HJM sing 173 n n C10 C4 HJM sing 174 n n C10 C14 HJM sing 175 n n C4 C6 HJM sing 176 n n C1 H2 HJM sing 177 n n N2 H3 HJM sing 178 n n C2 H4 HJM sing 179 n n C3 H5 HJM sing 180 n n C10 H6 HJM sing 181 n n C10 H7 HJM sing 182 n n C12 H8 HJM sing 183 n n C12 H9 HJM sing 184 n n C14 H10 HJM sing 185 n n C14 H11 HJM sing 186 n n C14 H12 HJM sing 187 n n C16 H13 HJM sing 188 n n C17 H14 HJM sing 189 n n C19 H15 HJM sing 190 n n C20 H16 HJM sing 191 n n C20 H17 HJM sing 192 n n C20 H18 HJM sing 193 n n C4 H19 HJM sing 194 n n C5 H20 HJM sing 195 n n C5 H21 HJM sing 196 n n C6 H22 HJM sing 197 n n C6 H23 HJM sing 198 n n C7 H24 HJM sing 199 n n C7 H25 HJM sing 200 n n C9 H26 HJM sing 201 n n C9 H27 HJM sing 202 n n # _atom_sites.entry_id 6DZY _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 6 HJM A 1 701 701 HJM HJM . G 7 LMT A 1 702 702 LMT LMT . # 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 N N1 HJM . . . F 6 161.272 152.951 173.361 1 139.28 ? N1 HJM 701 A 1 HETATM 2 C C1 HJM . . . F 6 161.532 152.616 174.871 1 139.28 ? C1 HJM 701 A 1 HETATM 3 N N2 HJM . . . F 6 160.835 148.966 175.587 1 139.28 ? N2 HJM 701 A 1 HETATM 4 C C2 HJM . . . F 6 160.724 151.481 175.396 1 139.28 ? C2 HJM 701 A 1 HETATM 5 C C3 HJM . . . F 6 159.025 153.07 174.358 1 139.28 ? C3 HJM 701 A 1 HETATM 6 O O HJM . . . F 6 163.094 145.287 172.062 1 139.28 ? O HJM 701 A 1 HETATM 7 C C10 HJM . . . F 6 162.136 154.964 175.44 1 139.28 ? C10 HJM 701 A 1 HETATM 8 C C11 HJM . . . F 6 161.746 149.837 173.706 1 139.28 ? C11 HJM 701 A 1 HETATM 9 C C12 HJM . . . F 6 161.969 150.694 172.409 1 139.28 ? C12 HJM 701 A 1 HETATM 10 C C13 HJM . . . F 6 161.817 148.416 173.661 1 139.28 ? C13 HJM 701 A 1 HETATM 11 C C14 HJM . . . F 6 163.322 154.773 176.464 1 139.28 ? C14 HJM 701 A 1 HETATM 12 C C15 HJM . . . F 6 161.298 147.891 174.852 1 139.28 ? C15 HJM 701 A 1 HETATM 13 C C16 HJM . . . F 6 162.232 147.487 172.668 1 139.28 ? C16 HJM 701 A 1 HETATM 14 C C17 HJM . . . F 6 161.322 146.563 175.213 1 139.28 ? C17 HJM 701 A 1 HETATM 15 C C18 HJM . . . F 6 162.358 146.122 172.998 1 139.28 ? C18 HJM 701 A 1 HETATM 16 C C19 HJM . . . F 6 161.849 145.648 174.24 1 139.28 ? C19 HJM 701 A 1 HETATM 17 C C20 HJM . . . F 6 163.061 143.823 172.353 1 139.28 ? C20 HJM 701 A 1 HETATM 18 C C4 HJM . . . F 6 161.106 153.907 175.629 1 139.28 ? C4 HJM 701 A 1 HETATM 19 C C5 HJM . . . F 6 159.234 151.776 175.179 1 139.28 ? C5 HJM 701 A 1 HETATM 20 C C6 HJM . . . F 6 159.615 154.243 175.09 1 139.28 ? C6 HJM 701 A 1 HETATM 21 C C7 HJM . . . F 6 159.776 152.863 173.037 1 139.28 ? C7 HJM 701 A 1 HETATM 22 C C8 HJM . . . F 6 161.147 150.127 174.895 1 139.28 ? C8 HJM 701 A 1 HETATM 23 C C9 HJM . . . F 6 162.195 152.213 172.455 1 139.28 ? C9 HJM 701 A 1 # _model_server_stats.io_time_ms 117 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #