data_206D # _model_server_result.job_id MyasJxbzUpmnkkNjjsIG-w _model_server_result.datetime_utc '2024-10-18 13:22:32' _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 206d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":14}' # _entry.id 206D # _exptl.entry_id 206D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 202.34 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMINE _entity.pdbx_number_of_molecules 2 _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 206D _cell.length_a 54.45 _cell.length_b 54.45 _cell.length_c 42.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 206D _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 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,F _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 C N N ? 3 D 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 hydrog 'DC-DG PAIR' hydrog1 A N4 DC 1 A DC 1 1_555 B O6 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N1 DG 2 A DG 2 1_555 B N3 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N2 DG 2 A DG 2 1_555 B O2 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A O6 DG 2 A DG 2 1_555 B N4 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N1 DG 3 A DG 3 1_555 B N3 DC 4 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N2 DG 3 A DG 3 1_555 B O2 DC 4 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O6 DG 3 A DG 3 1_555 B N4 DC 4 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog8 A O2 DT 4 A DT 4 1_555 B N6 DA 3 B DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog9 A N1 DG 5 A DG 5 1_555 B N3 DC 2 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 7 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 152 n n N1 HN11 SPM sing 153 n n N1 HN12 SPM sing 154 n n C2 C3 SPM sing 155 n n C2 H21 SPM sing 156 n n C2 H22 SPM sing 157 n n C3 C4 SPM sing 158 n n C3 H31 SPM sing 159 n n C3 H32 SPM sing 160 n n C4 N5 SPM sing 161 n n C4 H41 SPM sing 162 n n C4 H42 SPM sing 163 n n N5 C6 SPM sing 164 n n N5 HN5 SPM sing 165 n n C6 C7 SPM sing 166 n n C6 H61 SPM sing 167 n n C6 H62 SPM sing 168 n n C7 C8 SPM sing 169 n n C7 H71 SPM sing 170 n n C7 H72 SPM sing 171 n n C8 C9 SPM sing 172 n n C8 H81 SPM sing 173 n n C8 H82 SPM sing 174 n n C9 N10 SPM sing 175 n n C9 H91 SPM sing 176 n n C9 H92 SPM sing 177 n n N10 C11 SPM sing 178 n n N10 HN0 SPM sing 179 n n C11 C12 SPM sing 180 n n C11 H111 SPM sing 181 n n C11 H112 SPM sing 182 n n C12 C13 SPM sing 183 n n C12 H121 SPM sing 184 n n C12 H122 SPM sing 185 n n C13 N14 SPM sing 186 n n C13 H131 SPM sing 187 n n C13 H132 SPM sing 188 n n N14 HN41 SPM sing 189 n n N14 HN42 SPM sing 190 n n # _atom_sites.entry_id 206D _atom_sites.fract_transf_matrix[1][1] 0.018366 _atom_sites.fract_transf_matrix[1][2] 0.010604 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021207 _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] 0.023753 _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 3 SPM A 1 13 13 SPM SPM . D 3 SPM A 1 14 14 SPM SPM . E 4 HOH A 1 15 15 HOH HOH . E 4 HOH A 2 16 16 HOH HOH . E 4 HOH A 3 19 19 HOH HOH . E 4 HOH A 4 20 20 HOH HOH . E 4 HOH A 5 21 21 HOH HOH . E 4 HOH A 6 23 23 HOH HOH . E 4 HOH A 7 24 24 HOH HOH . E 4 HOH A 8 25 25 HOH HOH . E 4 HOH A 9 26 26 HOH HOH . E 4 HOH A 10 27 27 HOH HOH . E 4 HOH A 11 28 28 HOH HOH . E 4 HOH A 12 29 29 HOH HOH . E 4 HOH A 13 30 30 HOH HOH . E 4 HOH A 14 31 31 HOH HOH . F 4 HOH B 1 17 17 HOH HOH . F 4 HOH B 2 18 18 HOH HOH . F 4 HOH B 3 22 22 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 . . . D 3 44.637 11.394 14.269 1 40.97 ? N1 SPM 14 A 1 HETATM 2 C C2 SPM . . . D 3 45.56 10.336 13.644 1 37.47 ? C2 SPM 14 A 1 HETATM 3 C C3 SPM . . . D 3 44.815 9.031 13.838 1 41.2 ? C3 SPM 14 A 1 HETATM 4 C C4 SPM . . . D 3 45.824 8.019 14.31 1 40.22 ? C4 SPM 14 A 1 HETATM 5 N N5 SPM . . . D 3 45.025 7.266 15.376 1 41.8 ? N5 SPM 14 A 1 HETATM 6 C C6 SPM . . . D 3 46.097 6.607 16.266 1 44.41 ? C6 SPM 14 A 1 HETATM 7 C C7 SPM . . . D 3 45.48 6.072 17.587 0.5 39.84 ? C7 SPM 14 A 1 # _model_server_stats.io_time_ms 114 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 7 #