data_3R6R # _model_server_result.job_id ta3LxrvMMMvg22WX6bE5QA _model_server_result.datetime_utc '2024-10-15 00:21:14' _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 3r6r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":25}' # _entry.id 3R6R # _exptl.entry_id 3R6R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 336.361 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description BERBERINE _entity.pdbx_number_of_molecules 4 _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 3R6R _cell.length_a 65.62 _cell.length_b 65.62 _cell.length_c 41.81 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3R6R _symmetry.cell_setting ? _symmetry.Int_Tables_number 168 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G 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 metalc ? metalc1 B K K . A K 1 1_555 A O6 DG 3 A DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.97 ? metalc ? metalc2 B K K . A K 1 1_555 A O6 DG 4 A DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc3 B K K . A K 1 1_555 A O6 DG 9 A DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? metalc ? metalc4 B K K . A K 1 1_555 A O6 DG 10 A DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.777 ? metalc ? metalc5 B K K . A K 1 1_555 A O6 DG 15 A DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc6 B K K . A K 1 1_555 A O6 DG 16 A DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc7 B K K . A K 1 1_555 A O6 DG 21 A DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.912 ? metalc ? metalc8 B K K . A K 1 1_555 A O6 DG 22 A DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? metalc ? metalc9 B K K . A K 1 1_555 H O HOH . A HOH 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.278 ? metalc ? metalc10 A O6 DG 2 A DG 3 1_555 C K K . A K 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc11 A O6 DG 3 A DG 4 1_555 C K K . A K 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? metalc ? metalc12 A O6 DG 8 A DG 9 1_555 C K K . A K 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc13 A O6 DG 9 A DG 10 1_555 C K K . A K 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc14 A O6 DG 14 A DG 15 1_555 C K K . A K 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc15 A O6 DG 15 A DG 16 1_555 C K K . A K 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc16 A O6 DG 20 A DG 21 1_555 C K K . A K 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc17 A O6 DG 21 A DG 22 1_555 C K K . A K 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? hydrog TYPE_6_PAIR hydrog1 A N1 DG 2 A DG 3 1_555 A O6 DG 8 A DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog2 A N2 DG 2 A DG 3 1_555 A N7 DG 8 A DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog3 A N7 DG 2 A DG 3 1_555 A N2 DG 20 A DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog4 A O6 DG 2 A DG 3 1_555 A N1 DG 20 A DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog5 A N1 DG 3 A DG 4 1_555 A O6 DG 9 A DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog6 A N2 DG 3 A DG 4 1_555 A N7 DG 9 A DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog7 A N7 DG 3 A DG 4 1_555 A N2 DG 21 A DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog8 A O6 DG 3 A DG 4 1_555 A N1 DG 21 A DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog9 A N1 DG 4 A DG 5 1_555 A O6 DG 10 A DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog10 A N2 DG 4 A DG 5 1_555 A N7 DG 10 A DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog11 A N7 DG 4 A DG 5 1_555 A N2 DG 22 A DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog12 A O6 DG 4 A DG 5 1_555 A N1 DG 22 A DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog13 A N1 DG 8 A DG 9 1_555 A O6 DG 14 A DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog14 A N2 DG 8 A DG 9 1_555 A N7 DG 14 A DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog15 A N1 DG 9 A DG 10 1_555 A O6 DG 15 A DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog16 A N2 DG 9 A DG 10 1_555 A N7 DG 15 A DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog17 A N1 DG 10 A DG 11 1_555 A O6 DG 16 A DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog18 A N2 DG 10 A DG 11 1_555 A N7 DG 16 A DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog19 A N1 DG 14 A DG 15 1_555 A O6 DG 20 A DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog20 A N2 DG 14 A DG 15 1_555 A N7 DG 20 A DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog21 A N1 DG 15 A DG 16 1_555 A O6 DG 21 A DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog22 A N2 DG 15 A DG 16 1_555 A N7 DG 21 A DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog23 A N1 DG 16 A DG 17 1_555 A O6 DG 22 A DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog24 A N2 DG 16 A DG 17 1_555 A N7 DG 22 A DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C20 H18 N O4 1' _chem_comp.formula_weight 336.361 _chem_comp.id BER _chem_comp.mon_nstd_flag . _chem_comp.name BERBERINE _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 C1 C2 BER sing 1 n y C1 N1 BER doub 2 n y C1 C3 BER sing 3 n y C2 C4 BER doub 4 n y C2 C5 BER sing 5 n y N1 C6 BER sing 6 n y N1 C7 BER sing 7 n n C3 C8 BER doub 8 n y C3 H31 BER sing 9 n n C4 C9 BER sing 10 n y C4 C10 BER sing 11 n n C5 C11 BER doub 12 n y C5 H51 BER sing 13 n n C6 C12 BER doub 14 n y C6 H61 BER sing 15 n n C7 C10 BER sing 16 n n C7 H71 BER sing 17 n n C7 H72 BER sing 18 n n C8 C12 BER sing 19 n y C8 C13 BER sing 20 n y C9 C14 BER doub 21 n y C9 H91 BER sing 22 n n C10 H101 BER sing 23 n n C10 H102 BER sing 24 n n C11 C14 BER sing 25 n y C11 O1 BER sing 26 n n C12 C15 BER sing 27 n y C13 C16 BER doub 28 n y C13 H131 BER sing 29 n n C14 O2 BER sing 30 n n O1 C17 BER sing 31 n n C15 C18 BER doub 32 n y C15 O3 BER sing 33 n n C16 C18 BER sing 34 n y C16 H161 BER sing 35 n n O2 C17 BER sing 36 n n C17 H171 BER sing 37 n n C17 H172 BER sing 38 n n C18 O4 BER sing 39 n n O3 C19 BER sing 40 n n O4 C20 BER sing 41 n n C19 H191 BER sing 42 n n C19 H192 BER sing 43 n n C19 H193 BER sing 44 n n C20 H201 BER sing 45 n n C20 H202 BER sing 46 n n C20 H203 BER sing 47 n n # _atom_sites.entry_id 3R6R _atom_sites.fract_transf_matrix[1][1] 0.015239 _atom_sites.fract_transf_matrix[1][2] 0.008798 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017597 _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] 0.023918 _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 B 2 K A 1 1 1 K K . C 2 K A 1 24 2 K K . D 3 BER A 1 25 1 BER BER . E 3 BER A 1 26 1 BER BER . F 3 BER A 1 27 1 BER BER . G 3 BER A 1 28 1 BER BER . H 4 HOH A 1 29 29 HOH HOH . H 4 HOH A 2 30 1 HOH HOH . H 4 HOH A 3 31 2 HOH HOH . H 4 HOH A 4 32 3 HOH HOH . H 4 HOH A 5 33 4 HOH HOH . H 4 HOH A 6 34 5 HOH HOH . H 4 HOH A 7 35 6 HOH HOH . H 4 HOH A 8 36 7 HOH HOH . H 4 HOH A 9 37 8 HOH HOH . H 4 HOH A 10 38 9 HOH HOH . H 4 HOH A 11 39 10 HOH HOH . H 4 HOH A 12 40 11 HOH HOH . H 4 HOH A 13 41 12 HOH HOH . H 4 HOH A 14 42 13 HOH HOH . H 4 HOH A 15 43 14 HOH HOH . H 4 HOH A 16 44 15 HOH HOH . H 4 HOH A 17 45 16 HOH HOH . H 4 HOH A 18 46 17 HOH HOH . H 4 HOH A 19 47 18 HOH HOH . H 4 HOH A 20 48 19 HOH HOH . H 4 HOH A 21 49 20 HOH HOH . H 4 HOH A 22 50 21 HOH HOH . H 4 HOH A 23 51 22 HOH HOH . H 4 HOH A 24 52 23 HOH HOH . H 4 HOH A 25 53 24 HOH HOH . H 4 HOH A 26 54 25 HOH HOH . H 4 HOH A 27 55 26 HOH HOH . H 4 HOH A 28 56 27 HOH HOH . H 4 HOH A 29 57 28 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 BER . . . D 3 4.495 21.544 -1.967 1 21.81 ? C1 BER 25 A 1 HETATM 2 C C2 BER . . . D 3 4.147 22.698 -2.867 1 21.74 ? C2 BER 25 A 1 HETATM 3 N N1 BER . . . D 3 4.651 20.234 -2.517 1 21.94 ? N1 BER 25 A 1 HETATM 4 C C3 BER . . . D 3 4.629 21.723 -0.574 1 21.35 ? C3 BER 25 A 1 HETATM 5 C C4 BER . . . D 3 3.998 22.405 -4.335 1 22.29 ? C4 BER 25 A 1 HETATM 6 C C5 BER . . . D 3 3.968 23.995 -2.376 1 21.83 ? C5 BER 25 A 1 HETATM 7 C C6 BER . . . D 3 4.937 19.168 -1.748 1 21.85 ? C6 BER 25 A 1 HETATM 8 C C7 BER . . . D 3 4.522 19.906 -3.939 1 22.44 ? C7 BER 25 A 1 HETATM 9 C C8 BER . . . D 3 4.932 20.629 0.254 1 21.45 ? C8 BER 25 A 1 HETATM 10 C C9 BER . . . D 3 3.642 23.4 -5.245 1 21.55 ? C9 BER 25 A 1 HETATM 11 C C10 BER . . . D 3 4.164 21.021 -4.915 1 22.7 ? C10 BER 25 A 1 HETATM 12 C C11 BER . . . D 3 3.63 24.964 -3.315 1 22.51 ? C11 BER 25 A 1 HETATM 13 C C12 BER . . . D 3 5.087 19.296 -0.373 1 21.81 ? C12 BER 25 A 1 HETATM 14 C C13 BER . . . D 3 5.088 20.748 1.643 1 21.54 ? C13 BER 25 A 1 HETATM 15 C C14 BER . . . D 3 3.471 24.667 -4.733 1 22 ? C14 BER 25 A 1 HETATM 16 O O1 BER . . . D 3 3.389 26.295 -3.149 1 24.06 ? O1 BER 25 A 1 HETATM 17 C C15 BER . . . D 3 5.402 18.129 0.492 1 23.12 ? C15 BER 25 A 1 HETATM 18 C C16 BER . . . D 3 5.384 19.645 2.458 1 22 ? C16 BER 25 A 1 HETATM 19 O O2 BER . . . D 3 3.147 25.816 -5.376 1 22.77 ? O2 BER 25 A 1 HETATM 20 C C17 BER . . . D 3 3.069 26.894 -4.422 1 24.33 ? C17 BER 25 A 1 HETATM 21 C C18 BER . . . D 3 5.549 18.349 1.949 1 23.03 ? C18 BER 25 A 1 HETATM 22 O O3 BER . . . D 3 5.549 16.873 -0.034 1 25.27 ? O3 BER 25 A 1 HETATM 23 O O4 BER . . . D 3 5.847 17.263 2.749 1 24.64 ? O4 BER 25 A 1 HETATM 24 C C19 BER . . . D 3 4.572 15.848 0.172 1 26.81 ? C19 BER 25 A 1 HETATM 25 C C20 BER . . . D 3 5.878 17.419 4.174 1 24.71 ? C20 BER 25 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 47 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 2610 _model_server_stats.encode_time_ms 24 _model_server_stats.element_count 25 #