data_375D # _model_server_result.job_id '_NFHnRTO5ssEhKHnP56PCg' _model_server_result.datetime_utc '2025-01-11 10:01:01' _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 375d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":41}' # _entry.id 375D # _exptl.entry_id 375D _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 86.3 _cell.angle_beta 84.5 _cell.angle_gamma 68.58 _cell.entry_id 375D _cell.length_a 32.56 _cell.length_b 32.59 _cell.length_c 37.64 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 375D _symmetry.cell_setting triclinic _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 # _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 75 n n C1 N2 NT sing 76 n n C1 N3 NT sing 77 n n N1 HN1 NT sing 78 n n N2 HN21 NT sing 79 n n N2 HN22 NT sing 80 n n N3 C2 NT sing 81 n n N3 HN3 NT sing 82 n n C2 C3 NT sing 83 n n C2 H21 NT sing 84 n n C2 H22 NT sing 85 n n C3 O1 NT doub 86 n n C3 N4 NT sing 87 n n N4 C4 NT sing 88 n n N4 HN4 NT sing 89 n n C4 C5 NT sing 90 n y C4 C7 NT doub 91 n y C5 C6 NT doub 92 n y C5 H5 NT sing 93 n n C6 N5 NT sing 94 n y C6 C9 NT sing 95 n n N5 C8 NT sing 96 n n N5 C7 NT sing 97 n y C8 H81 NT sing 98 n n C8 H82 NT sing 99 n n C8 H83 NT sing 100 n n C7 H7 NT sing 101 n n C9 O2 NT doub 102 n n C9 N6 NT sing 103 n n N6 C10 NT sing 104 n n N6 HN6 NT sing 105 n n C10 C11 NT sing 106 n y C10 C13 NT doub 107 n y C11 C12 NT doub 108 n y C11 H11 NT sing 109 n n C12 N7 NT sing 110 n y C12 C15 NT sing 111 n n N7 C14 NT sing 112 n n N7 C13 NT sing 113 n y C14 H141 NT sing 114 n n C14 H142 NT sing 115 n n C14 H143 NT sing 116 n n C13 H13 NT sing 117 n n C15 O3 NT doub 118 n n C15 N8 NT sing 119 n n N8 C16 NT sing 120 n n N8 HN8 NT sing 121 n n C16 C17 NT sing 122 n n C16 H161 NT sing 123 n n C16 H162 NT sing 124 n n C17 C18 NT sing 125 n n C17 H171 NT sing 126 n n C17 H172 NT sing 127 n n C18 N9 NT doub 128 n n C18 N10 NT sing 129 n n N9 HN9 NT sing 130 n n N10 HN01 NT sing 131 n n N10 HN02 NT sing 132 n n # _atom_sites.entry_id 375D _atom_sites.fract_transf_matrix[1][1] 0.030713 _atom_sites.fract_transf_matrix[1][2] -0.012048 _atom_sites.fract_transf_matrix[1][3] -0.002575 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.032961 _atom_sites.fract_transf_matrix[2][3] -0.001051 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.026704 _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 49 49 HOH HOH . I 3 HOH A 2 52 52 HOH HOH . I 3 HOH A 3 55 55 HOH HOH . I 3 HOH A 4 65 65 HOH HOH . I 3 HOH A 5 66 66 HOH HOH . I 3 HOH A 6 67 67 HOH HOH . I 3 HOH A 7 69 69 HOH HOH . I 3 HOH A 8 70 70 HOH HOH . I 3 HOH A 9 72 72 HOH HOH . I 3 HOH A 10 73 73 HOH HOH . I 3 HOH A 11 75 75 HOH HOH . I 3 HOH A 12 79 79 HOH HOH . I 3 HOH A 13 81 81 HOH HOH . I 3 HOH A 14 83 83 HOH HOH . I 3 HOH A 15 84 84 HOH HOH . I 3 HOH A 16 85 85 HOH HOH . I 3 HOH A 17 86 86 HOH HOH . I 3 HOH A 18 89 89 HOH HOH . J 3 HOH B 1 46 46 HOH HOH . J 3 HOH B 2 47 47 HOH HOH . J 3 HOH B 3 50 50 HOH HOH . J 3 HOH B 4 53 53 HOH HOH . J 3 HOH B 5 54 54 HOH HOH . J 3 HOH B 6 57 57 HOH HOH . J 3 HOH B 7 58 58 HOH HOH . J 3 HOH B 8 59 59 HOH HOH . J 3 HOH B 9 68 68 HOH HOH . J 3 HOH B 10 80 80 HOH HOH . J 3 HOH B 11 87 87 HOH HOH . J 3 HOH B 12 91 91 HOH HOH . J 3 HOH B 13 92 92 HOH HOH . K 3 HOH C 1 45 45 HOH HOH . K 3 HOH C 2 48 48 HOH HOH . K 3 HOH C 3 51 51 HOH HOH . K 3 HOH C 4 56 56 HOH HOH . K 3 HOH C 5 61 61 HOH HOH . K 3 HOH C 6 62 62 HOH HOH . K 3 HOH C 7 63 63 HOH HOH . K 3 HOH C 8 64 64 HOH HOH . K 3 HOH C 9 71 71 HOH HOH . K 3 HOH C 10 74 74 HOH HOH . K 3 HOH C 11 76 76 HOH HOH . K 3 HOH C 12 77 77 HOH HOH . K 3 HOH C 13 82 82 HOH HOH . K 3 HOH C 14 88 88 HOH HOH . K 3 HOH C 15 93 93 HOH HOH . L 3 HOH D 1 60 60 HOH HOH . L 3 HOH D 2 78 78 HOH HOH . L 3 HOH D 3 90 90 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 7.577 2.276 -6.501 1 49.4 ? C1 NT 41 A 1 HETATM 2 N N1 NT . . . E 2 7.322 3.505 -6.946 1 51.93 ? N1 NT 41 A 1 HETATM 3 N N2 NT . . . E 2 8.746 1.949 -5.903 1 48.89 ? N2 NT 41 A 1 HETATM 4 N N3 NT . . . E 2 6.605 1.395 -6.729 1 46.9 ? N3 NT 41 A 1 HETATM 5 C C2 NT . . . E 2 7.075 0.058 -6.606 1 44.92 ? C2 NT 41 A 1 HETATM 6 C C3 NT . . . E 2 6.13 -0.948 -7.199 1 44.72 ? C3 NT 41 A 1 HETATM 7 O O1 NT . . . E 2 6.106 -1.177 -8.409 1 45.47 ? O1 NT 41 A 1 HETATM 8 N N4 NT . . . E 2 5.348 -1.491 -6.248 1 42.82 ? N4 NT 41 A 1 HETATM 9 C C4 NT . . . E 2 4.48 -2.55 -6.505 1 39.37 ? C4 NT 41 A 1 HETATM 10 C C5 NT . . . E 2 3.609 -3.143 -5.618 1 38.44 ? C5 NT 41 A 1 HETATM 11 C C6 NT . . . E 2 3.084 -4.274 -6.174 1 35.56 ? C6 NT 41 A 1 HETATM 12 N N5 NT . . . E 2 3.615 -4.339 -7.414 1 36.64 ? N5 NT 41 A 1 HETATM 13 C C8 NT . . . E 2 3.432 -5.404 -8.475 1 37.4 ? C8 NT 41 A 1 HETATM 14 C C7 NT . . . E 2 4.461 -3.348 -7.666 1 37.19 ? C7 NT 41 A 1 HETATM 15 C C9 NT . . . E 2 2.212 -5.275 -5.569 1 35.27 ? C9 NT 41 A 1 HETATM 16 O O2 NT . . . E 2 2.106 -6.404 -6.024 1 33.31 ? O2 NT 41 A 1 HETATM 17 N N6 NT . . . E 2 1.561 -4.92 -4.455 1 34.81 ? N6 NT 41 A 1 HETATM 18 C C10 NT . . . E 2 0.744 -5.831 -3.798 1 34.88 ? C10 NT 41 A 1 HETATM 19 C C11 NT . . . E 2 -0.073 -5.616 -2.691 1 37.9 ? C11 NT 41 A 1 HETATM 20 C C12 NT . . . E 2 -0.721 -6.781 -2.299 1 36.99 ? C12 NT 41 A 1 HETATM 21 N N7 NT . . . E 2 -0.327 -7.717 -3.188 1 36.82 ? N7 NT 41 A 1 HETATM 22 C C14 NT . . . E 2 -0.74 -9.182 -3.255 1 37.38 ? C14 NT 41 A 1 HETATM 23 C C13 NT . . . E 2 0.55 -7.201 -4.072 1 35.47 ? C13 NT 41 A 1 HETATM 24 C C15 NT . . . E 2 -1.654 -7.051 -1.22 1 38.11 ? C15 NT 41 A 1 HETATM 25 O O3 NT . . . E 2 -2.033 -8.188 -0.954 1 35.48 ? O3 NT 41 A 1 HETATM 26 N N8 NT . . . E 2 -2.081 -5.931 -0.597 1 41.29 ? N8 NT 41 A 1 HETATM 27 C C16 NT . . . E 2 -3.028 -5.958 0.512 1 45.07 ? C16 NT 41 A 1 HETATM 28 C C17 NT . . . E 2 -2.936 -7.175 1.433 1 46.32 ? C17 NT 41 A 1 HETATM 29 C C18 NT . . . E 2 -4.03 -7.064 2.509 1 49.8 ? C18 NT 41 A 1 HETATM 30 N N9 NT . . . E 2 -4.831 -5.998 2.682 1 47.3 ? N9 NT 41 A 1 HETATM 31 N N10 NT . . . E 2 -3.937 -8.257 3.18 1 49.74 ? N10 NT 41 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #