data_2O3Y # _model_server_result.job_id ELrVttOijGDOTNDgBjY5aA _model_server_result.datetime_utc '2024-11-27 19:59:39' _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 2o3y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":51}' # _entry.id 2O3Y # _exptl.entry_id 2O3Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 202.34 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMINE _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 2O3Y _cell.length_a 47.94 _cell.length_b 49.23 _cell.length_c 57.46 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2O3Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 hydrog WATSON-CRICK hydrog1 A N1 G 3 A G 3 1_555 B N3 C 23 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 3 A G 3 1_555 B O2 C 23 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 3 A G 3 1_555 B N4 C 23 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 C 4 A C 4 1_555 B N1 G 22 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 C 4 A C 4 1_555 B O6 G 22 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 C 4 A C 4 1_555 B N2 G 22 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 G 5 A G 5 1_555 B N3 C 21 B C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 G 5 A G 5 1_555 B O2 C 21 B C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 G 5 A G 5 1_555 B N4 C 21 B C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog10 A N3 U 6 A U 6 1_555 B O4 U 20 B U 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog11 A O2 U 6 A U 6 1_555 B N3 U 20 B U 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 C 7 A C 7 1_555 B N1 G 19 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N4 C 7 A C 7 1_555 B O6 G 19 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O2 C 7 A C 7 1_555 B N2 G 19 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog15 A N4 C 9 A C 9 1_555 B N1 A 16 B A 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 U 10 A U 10 1_555 B N1 A 15 B A 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O4 U 10 A U 10 1_555 B N6 A 15 B A 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N3 C 11 A C 11 1_555 B N1 G 14 B G 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N4 C 11 A C 11 1_555 B O6 G 14 B G 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O2 C 11 A C 11 1_555 B N2 G 14 B G 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N3 C 12 A C 12 1_555 B N1 G 13 B G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N4 C 12 A C 12 1_555 B O6 G 13 B G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O2 C 12 A C 12 1_555 B N2 G 13 B G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N1 G 13 A G 13 1_555 B N3 C 12 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N2 G 13 A G 13 1_555 B O2 C 12 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O6 G 13 A G 13 1_555 B N4 C 12 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N1 G 14 A G 14 1_555 B N3 C 11 B C 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N2 G 14 A G 14 1_555 B O2 C 11 B C 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A O6 G 14 A G 14 1_555 B N4 C 11 B C 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N1 A 15 A A 15 1_555 B N3 U 10 B U 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N6 A 15 A A 15 1_555 B O4 U 10 B U 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-C MISPAIR' hydrog32 A N3 A 17 A A 17 1_555 B N4 C 9 B C 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-G MISPAIR' hydrog33 A N7 A 18 A A 18 1_555 B N2 G 8 B G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A N1 G 19 A G 19 1_555 B N3 C 7 B C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A N2 G 19 A G 19 1_555 B O2 C 7 B C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A O6 G 19 A G 19 1_555 B N4 C 7 B C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog37 A N3 U 20 A U 20 1_555 B O2 U 6 B U 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog38 A O4 U 20 A U 20 1_555 B N3 U 6 B U 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 A N3 C 21 A C 21 1_555 B N1 G 5 B G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 A N4 C 21 A C 21 1_555 B O6 G 5 B G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 A O2 C 21 A C 21 1_555 B N2 G 5 B G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 A N1 G 22 A G 22 1_555 B N3 C 4 B C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 A N2 G 22 A G 22 1_555 B O2 C 4 B C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 A O6 G 22 A G 22 1_555 B N4 C 4 B C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 A N3 C 23 A C 23 1_555 B N1 G 3 B G 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 A N4 C 23 A C 23 1_555 B O6 G 3 B G 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog47 A O2 C 23 A C 23 1_555 B N2 G 3 B G 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H26 N4' _chem_comp.formula_weight 202.34 _chem_comp.id SPM _chem_comp.mon_nstd_flag . _chem_comp.name SPERMINE _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 N1 C2 SPM sing 118 n n N1 HN11 SPM sing 119 n n N1 HN12 SPM sing 120 n n C2 C3 SPM sing 121 n n C2 H21 SPM sing 122 n n C2 H22 SPM sing 123 n n C3 C4 SPM sing 124 n n C3 H31 SPM sing 125 n n C3 H32 SPM sing 126 n n C4 N5 SPM sing 127 n n C4 H41 SPM sing 128 n n C4 H42 SPM sing 129 n n N5 C6 SPM sing 130 n n N5 HN5 SPM sing 131 n n C6 C7 SPM sing 132 n n C6 H61 SPM sing 133 n n C6 H62 SPM sing 134 n n C7 C8 SPM sing 135 n n C7 H71 SPM sing 136 n n C7 H72 SPM sing 137 n n C8 C9 SPM sing 138 n n C8 H81 SPM sing 139 n n C8 H82 SPM sing 140 n n C9 N10 SPM sing 141 n n C9 H91 SPM sing 142 n n C9 H92 SPM sing 143 n n N10 C11 SPM sing 144 n n N10 HN0 SPM sing 145 n n C11 C12 SPM sing 146 n n C11 H111 SPM sing 147 n n C11 H112 SPM sing 148 n n C12 C13 SPM sing 149 n n C12 H121 SPM sing 150 n n C12 H122 SPM sing 151 n n C13 N14 SPM sing 152 n n C13 H131 SPM sing 153 n n C13 H132 SPM sing 154 n n N14 HN41 SPM sing 155 n n N14 HN42 SPM sing 156 n n # _atom_sites.entry_id 2O3Y _atom_sites.fract_transf_matrix[1][1] 0.020859 _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] 0.020313 _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] 0.017403 _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 C 2 SPM A 1 51 51 SPM SPM . D 3 HOH A 1 52 102 HOH HOH . D 3 HOH A 2 53 104 HOH HOH . D 3 HOH A 3 54 105 HOH HOH . D 3 HOH A 4 55 107 HOH HOH . D 3 HOH A 5 56 110 HOH HOH . D 3 HOH A 6 57 111 HOH HOH . D 3 HOH A 7 58 114 HOH HOH . D 3 HOH A 8 59 115 HOH HOH . D 3 HOH A 9 60 116 HOH HOH . D 3 HOH A 10 61 117 HOH HOH . D 3 HOH A 11 62 119 HOH HOH . D 3 HOH A 12 63 123 HOH HOH . D 3 HOH A 13 64 124 HOH HOH . D 3 HOH A 14 65 125 HOH HOH . D 3 HOH A 15 66 126 HOH HOH . D 3 HOH A 16 67 129 HOH HOH . D 3 HOH A 17 68 130 HOH HOH . D 3 HOH A 18 69 131 HOH HOH . D 3 HOH A 19 70 134 HOH HOH . D 3 HOH A 20 71 135 HOH HOH . D 3 HOH A 21 72 138 HOH HOH . D 3 HOH A 22 73 139 HOH HOH . D 3 HOH A 23 74 140 HOH HOH . D 3 HOH A 24 75 143 HOH HOH . D 3 HOH A 25 76 145 HOH HOH . D 3 HOH A 26 77 146 HOH HOH . D 3 HOH A 27 78 147 HOH HOH . D 3 HOH A 28 79 149 HOH HOH . D 3 HOH A 29 80 150 HOH HOH . D 3 HOH A 30 81 152 HOH HOH . D 3 HOH A 31 82 153 HOH HOH . D 3 HOH A 32 83 154 HOH HOH . D 3 HOH A 33 84 156 HOH HOH . E 3 HOH B 1 47 101 HOH HOH . E 3 HOH B 2 48 103 HOH HOH . E 3 HOH B 3 49 106 HOH HOH . E 3 HOH B 4 50 108 HOH HOH . E 3 HOH B 5 51 109 HOH HOH . E 3 HOH B 6 52 112 HOH HOH . E 3 HOH B 7 53 113 HOH HOH . E 3 HOH B 8 54 118 HOH HOH . E 3 HOH B 9 55 120 HOH HOH . E 3 HOH B 10 56 121 HOH HOH . E 3 HOH B 11 57 122 HOH HOH . E 3 HOH B 12 58 127 HOH HOH . E 3 HOH B 13 59 128 HOH HOH . E 3 HOH B 14 60 132 HOH HOH . E 3 HOH B 15 61 133 HOH HOH . E 3 HOH B 16 62 136 HOH HOH . E 3 HOH B 17 63 137 HOH HOH . E 3 HOH B 18 64 141 HOH HOH . E 3 HOH B 19 65 142 HOH HOH . E 3 HOH B 20 66 144 HOH HOH . E 3 HOH B 21 67 148 HOH HOH . E 3 HOH B 22 68 151 HOH HOH . E 3 HOH B 23 69 155 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 N N1 SPM . . . C 2 10.536 14.601 14.244 1 86.72 ? N1 SPM 51 A 1 HETATM 2 C C2 SPM . . . C 2 11.337 13.481 14.756 1 86.49 ? C2 SPM 51 A 1 HETATM 3 C C3 SPM . . . C 2 11.72 12.564 13.599 1 86.6 ? C3 SPM 51 A 1 HETATM 4 C C4 SPM . . . C 2 12.889 11.695 14.033 1 87.75 ? C4 SPM 51 A 1 HETATM 5 N N5 SPM . . . C 2 12.452 10.295 14.077 1 89.43 ? N5 SPM 51 A 1 HETATM 6 C C6 SPM . . . C 2 13.466 9.505 13.357 1 89.68 ? C6 SPM 51 A 1 HETATM 7 C C7 SPM . . . C 2 12.901 8.983 12.031 1 91.95 ? C7 SPM 51 A 1 HETATM 8 C C8 SPM . . . C 2 14.053 8.892 11.019 1 92.64 ? C8 SPM 51 A 1 HETATM 9 C C9 SPM . . . C 2 13.693 9.597 9.778 1 93.32 ? C9 SPM 51 A 1 HETATM 10 N N10 SPM . . . C 2 14.037 11.022 9.959 1 93.67 ? N10 SPM 51 A 1 HETATM 11 C C11 SPM . . . C 2 15.517 11.254 9.634 1 93.24 ? C11 SPM 51 A 1 HETATM 12 C C12 SPM . . . C 2 16.034 12.465 10.42 1 93.22 ? C12 SPM 51 A 1 HETATM 13 C C13 SPM . . . C 2 17.44 12.243 10.809 1 94.55 ? C13 SPM 51 A 1 HETATM 14 N N14 SPM . . . C 2 17.943 13.419 11.551 1 96.92 ? N14 SPM 51 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #