data_474D # _model_server_result.job_id hgYORWXLNQjp46Mkay1a8A _model_server_result.datetime_utc '2025-01-11 09:48:51' _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 474d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":41}' # _entry.id 474D # _exptl.entry_id 474D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 430.464 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NETROPSIN _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 86.01 _cell.angle_beta 84.37 _cell.angle_gamma 68.9 _cell.entry_id 474D _cell.length_a 32.66 _cell.length_b 32.77 _cell.length_c 37.71 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 474D _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,I,J 1 1 C,D,G,H,K,L 2 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 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 O3' DC 3 A DC 3 1_555 A P CBR 4 A CBR 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale2 A O3' CBR 4 A CBR 4 1_555 A P DC 5 A DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.577 ? covale ? covale3 B O3' DC 3 B DC 13 1_555 B P CBR 4 B CBR 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.615 ? covale ? covale4 B O3' CBR 4 B CBR 14 1_555 B P DC 5 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.59 ? covale ? covale5 C O3' DC 3 C DC 23 1_555 C P CBR 4 C CBR 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale6 C O3' CBR 4 C CBR 24 1_555 C P DC 5 C DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.589 ? covale ? covale7 D O3' DC 3 D DC 33 1_555 D P CBR 4 D CBR 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.586 ? covale ? covale8 D O3' CBR 4 D CBR 34 1_555 D P DC 5 D DC 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.594 ? # _chem_comp.formula 'C18 H26 N10 O3' _chem_comp.formula_weight 430.464 _chem_comp.id NT _chem_comp.mon_nstd_flag . _chem_comp.name NETROPSIN _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 N1 NT doub 110 n n C1 N2 NT sing 111 n n C1 N3 NT sing 112 n n N1 HN1 NT sing 113 n n N2 HN21 NT sing 114 n n N2 HN22 NT sing 115 n n N3 C2 NT sing 116 n n N3 HN3 NT sing 117 n n C2 C3 NT sing 118 n n C2 H21 NT sing 119 n n C2 H22 NT sing 120 n n C3 O1 NT doub 121 n n C3 N4 NT sing 122 n n N4 C4 NT sing 123 n n N4 HN4 NT sing 124 n n C4 C5 NT sing 125 n y C4 C7 NT doub 126 n y C5 C6 NT doub 127 n y C5 H5 NT sing 128 n n C6 N5 NT sing 129 n y C6 C9 NT sing 130 n n N5 C8 NT sing 131 n n N5 C7 NT sing 132 n y C8 H81 NT sing 133 n n C8 H82 NT sing 134 n n C8 H83 NT sing 135 n n C7 H7 NT sing 136 n n C9 O2 NT doub 137 n n C9 N6 NT sing 138 n n N6 C10 NT sing 139 n n N6 HN6 NT sing 140 n n C10 C11 NT sing 141 n y C10 C13 NT doub 142 n y C11 C12 NT doub 143 n y C11 H11 NT sing 144 n n C12 N7 NT sing 145 n y C12 C15 NT sing 146 n n N7 C14 NT sing 147 n n N7 C13 NT sing 148 n y C14 H141 NT sing 149 n n C14 H142 NT sing 150 n n C14 H143 NT sing 151 n n C13 H13 NT sing 152 n n C15 O3 NT doub 153 n n C15 N8 NT sing 154 n n N8 C16 NT sing 155 n n N8 HN8 NT sing 156 n n C16 C17 NT sing 157 n n C16 H161 NT sing 158 n n C16 H162 NT sing 159 n n C17 C18 NT sing 160 n n C17 H171 NT sing 161 n n C17 H172 NT sing 162 n n C18 N9 NT doub 163 n n C18 N10 NT sing 164 n n N9 HN9 NT sing 165 n n N10 HN01 NT sing 166 n n N10 HN02 NT sing 167 n n # _atom_sites.entry_id 474D _atom_sites.fract_transf_matrix[1][1] 0.030618 _atom_sites.fract_transf_matrix[1][2] -0.011815 _atom_sites.fract_transf_matrix[1][3] -0.002584 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.032709 _atom_sites.fract_transf_matrix[2][3] -0.001208 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.026665 _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 2 NT A 1 41 41 NT NT . F 2 NT A 1 42 42 NT NT . G 2 NT C 1 43 43 NT NT . H 2 NT C 1 44 44 NT NT . I 3 HOH A 1 46 46 HOH HOH . I 3 HOH A 2 49 49 HOH HOH . I 3 HOH A 3 50 50 HOH HOH . I 3 HOH A 4 52 52 HOH HOH . I 3 HOH A 5 55 55 HOH HOH . I 3 HOH A 6 60 60 HOH HOH . I 3 HOH A 7 61 61 HOH HOH . I 3 HOH A 8 65 65 HOH HOH . I 3 HOH A 9 66 66 HOH HOH . I 3 HOH A 10 74 74 HOH HOH . I 3 HOH A 11 75 75 HOH HOH . I 3 HOH A 12 76 76 HOH HOH . I 3 HOH A 13 77 77 HOH HOH . I 3 HOH A 14 82 82 HOH HOH . J 3 HOH B 1 47 47 HOH HOH . J 3 HOH B 2 48 48 HOH HOH . J 3 HOH B 3 51 51 HOH HOH . J 3 HOH B 4 57 57 HOH HOH . J 3 HOH B 5 63 63 HOH HOH . J 3 HOH B 6 64 64 HOH HOH . J 3 HOH B 7 71 71 HOH HOH . J 3 HOH B 8 73 73 HOH HOH . J 3 HOH B 9 78 78 HOH HOH . J 3 HOH B 10 81 81 HOH HOH . K 3 HOH C 1 45 45 HOH HOH . K 3 HOH C 2 53 53 HOH HOH . K 3 HOH C 3 54 54 HOH HOH . K 3 HOH C 4 56 56 HOH HOH . K 3 HOH C 5 59 59 HOH HOH . K 3 HOH C 6 62 62 HOH HOH . K 3 HOH C 7 68 68 HOH HOH . K 3 HOH C 8 69 69 HOH HOH . K 3 HOH C 9 70 70 HOH HOH . K 3 HOH C 10 72 72 HOH HOH . K 3 HOH C 11 79 79 HOH HOH . L 3 HOH D 1 58 58 HOH HOH . L 3 HOH D 2 67 67 HOH HOH . L 3 HOH D 3 80 80 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 NT . . . E 2 7.652 2.147 -6.501 1 58.54 ? C1 NT 41 A 1 HETATM 2 N N1 NT . . . E 2 7.41 3.446 -6.744 1 59.41 ? N1 NT 41 A 1 HETATM 3 N N2 NT . . . E 2 8.848 1.688 -6.032 1 58.48 ? N2 NT 41 A 1 HETATM 4 N N3 NT . . . E 2 6.632 1.327 -6.743 1 56.74 ? N3 NT 41 A 1 HETATM 5 C C2 NT . . . E 2 7.064 -0.031 -6.685 1 55.13 ? C2 NT 41 A 1 HETATM 6 C C3 NT . . . E 2 6.221 -1.073 -7.363 1 54.17 ? C3 NT 41 A 1 HETATM 7 O O1 NT . . . E 2 6.476 -1.145 -8.557 1 55.4 ? O1 NT 41 A 1 HETATM 8 N N4 NT . . . E 2 5.337 -1.77 -6.616 1 51.98 ? N4 NT 41 A 1 HETATM 9 C C4 NT . . . E 2 4.512 -2.858 -6.866 1 49.17 ? C4 NT 41 A 1 HETATM 10 C C5 NT . . . E 2 3.763 -3.428 -5.865 1 47.97 ? C5 NT 41 A 1 HETATM 11 C C6 NT . . . E 2 3.158 -4.546 -6.343 1 47.06 ? C6 NT 41 A 1 HETATM 12 N N5 NT . . . E 2 3.517 -4.671 -7.633 1 47.87 ? N5 NT 41 A 1 HETATM 13 C C8 NT . . . E 2 3.115 -5.772 -8.606 1 48.01 ? C8 NT 41 A 1 HETATM 14 C C7 NT . . . E 2 4.33 -3.679 -8 1 48.43 ? C7 NT 41 A 1 HETATM 15 C C9 NT . . . E 2 2.3 -5.511 -5.688 1 46.62 ? C9 NT 41 A 1 HETATM 16 O O2 NT . . . E 2 2.111 -6.594 -6.217 1 45.98 ? O2 NT 41 A 1 HETATM 17 N N6 NT . . . E 2 1.727 -5.162 -4.528 1 46.17 ? N6 NT 41 A 1 HETATM 18 C C10 NT . . . E 2 0.883 -6.049 -3.858 1 45.76 ? C10 NT 41 A 1 HETATM 19 C C11 NT . . . E 2 0.138 -5.81 -2.724 1 46.22 ? C11 NT 41 A 1 HETATM 20 C C12 NT . . . E 2 -0.586 -6.955 -2.425 1 46.13 ? C12 NT 41 A 1 HETATM 21 N N7 NT . . . E 2 -0.295 -7.894 -3.334 1 46.87 ? N7 NT 41 A 1 HETATM 22 C C14 NT . . . E 2 -0.849 -9.302 -3.452 1 47.78 ? C14 NT 41 A 1 HETATM 23 C C13 NT . . . E 2 0.574 -7.393 -4.198 1 46.35 ? C13 NT 41 A 1 HETATM 24 C C15 NT . . . E 2 -1.617 -7.206 -1.44 1 46.29 ? C15 NT 41 A 1 HETATM 25 O O3 NT . . . E 2 -2.088 -8.315 -1.215 1 45.95 ? O3 NT 41 A 1 HETATM 26 N N8 NT . . . E 2 -2.043 -6.054 -0.919 1 47.69 ? N8 NT 41 A 1 HETATM 27 C C16 NT . . . E 2 -3.138 -6.001 0.018 1 48.46 ? C16 NT 41 A 1 HETATM 28 C C17 NT . . . E 2 -3.08 -7.14 1.026 1 48.67 ? C17 NT 41 A 1 HETATM 29 C C18 NT . . . E 2 -4.075 -6.977 2.141 1 49.63 ? C18 NT 41 A 1 HETATM 30 N N9 NT . . . E 2 -4.831 -5.855 2.292 1 49.1 ? N9 NT 41 A 1 HETATM 31 N N10 NT . . . E 2 -3.938 -8.059 2.911 1 50.11 ? N10 NT 41 A 1 # _model_server_stats.io_time_ms 4 _model_server_stats.parse_time_ms 4 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #