data_355D # _model_server_result.job_id 1LapSEB691lx5evpbO_76Q _model_server_result.datetime_utc '2024-12-26 22:43:19' _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 355d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":26}' # _entry.id 355D # _exptl.entry_id 355D _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 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 355D _cell.length_a 25.186 _cell.length_b 40.208 _cell.length_c 65.656 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 355D _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 metalc ? metalc1 C MG MG . A MG 25 1_555 E O HOH . A HOH 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc2 C MG MG . A MG 25 1_555 E O HOH . A HOH 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc3 C MG MG . A MG 25 1_555 E O HOH . A HOH 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc4 C MG MG . A MG 25 1_555 F O HOH . B HOH 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc5 C MG MG . A MG 25 1_555 F O HOH . B HOH 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc6 C MG MG . A MG 25 1_555 F O HOH . B HOH 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DA 5 A DA 5 1_555 B N3 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 DA 5 A DA 5 1_555 B O4 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 DA 6 A DA 6 1_555 B N3 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N6 DA 6 A DA 6 1_555 B O4 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N3 DT 7 A DT 7 1_555 B N1 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O4 DT 7 A DT 7 1_555 B N6 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N3 DT 8 A DT 8 1_555 B N1 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O4 DT 8 A DT 8 1_555 B N6 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N3 DC 9 A DC 9 1_555 B N1 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N4 DC 9 A DC 9 1_555 B O6 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O2 DC 9 A DC 9 1_555 B N2 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N1 DG 10 A DG 10 1_555 B N3 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N2 DG 10 A DG 10 1_555 B O2 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O6 DG 10 A DG 10 1_555 B N4 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 DC 11 A DC 11 1_555 B N1 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N4 DC 11 A DC 11 1_555 B O6 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A O2 DC 11 A DC 11 1_555 B N2 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N1 DG 12 A DG 12 1_555 B N3 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N2 DG 12 A DG 12 1_555 B O2 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A O6 DG 12 A DG 12 1_555 B N4 DC 1 B DC 13 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 ? # _atom_sites.entry_id 355D _atom_sites.fract_transf_matrix[1][1] 0.039705 _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] 0.024871 _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] 0.015231 _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 MG A 1 25 25 MG MO6 . D 3 SPM B 1 26 26 SPM SPM . E 4 HOH A 1 28 28 HOH HOH . E 4 HOH A 2 29 29 HOH HOH . E 4 HOH A 3 31 31 HOH HOH . E 4 HOH A 4 32 32 HOH HOH . E 4 HOH A 5 33 33 HOH HOH . E 4 HOH A 6 35 35 HOH HOH . E 4 HOH A 7 36 36 HOH HOH . E 4 HOH A 8 39 39 HOH HOH . E 4 HOH A 9 40 40 HOH HOH . E 4 HOH A 10 41 41 HOH HOH . E 4 HOH A 11 42 42 HOH HOH . E 4 HOH A 12 47 47 HOH HOH . E 4 HOH A 13 49 49 HOH HOH . E 4 HOH A 14 51 51 HOH HOH . E 4 HOH A 15 52 52 HOH HOH . E 4 HOH A 16 53 53 HOH HOH . E 4 HOH A 17 54 54 HOH HOH . E 4 HOH A 18 55 55 HOH HOH . E 4 HOH A 19 57 57 HOH HOH . E 4 HOH A 20 58 58 HOH HOH . E 4 HOH A 21 59 59 HOH HOH . E 4 HOH A 22 60 60 HOH HOH . E 4 HOH A 23 62 62 HOH HOH . E 4 HOH A 24 64 64 HOH HOH . E 4 HOH A 25 65 65 HOH HOH . E 4 HOH A 26 66 66 HOH HOH . E 4 HOH A 27 67 67 HOH HOH . E 4 HOH A 28 68 68 HOH HOH . E 4 HOH A 29 69 69 HOH HOH . E 4 HOH A 30 71 71 HOH HOH . E 4 HOH A 31 72 72 HOH HOH . E 4 HOH A 32 76 76 HOH HOH . E 4 HOH A 33 78 78 HOH HOH . E 4 HOH A 34 80 80 HOH HOH . E 4 HOH A 35 84 84 HOH HOH . E 4 HOH A 36 86 86 HOH HOH . E 4 HOH A 37 87 87 HOH HOH . E 4 HOH A 38 91 91 HOH HOH . E 4 HOH A 39 92 92 HOH HOH . E 4 HOH A 40 95 95 HOH HOH . E 4 HOH A 41 96 96 HOH HOH . E 4 HOH A 42 97 97 HOH HOH . E 4 HOH A 43 98 98 HOH HOH . E 4 HOH A 44 99 99 HOH HOH . E 4 HOH A 45 100 100 HOH HOH . E 4 HOH A 46 101 101 HOH HOH . E 4 HOH A 47 102 102 HOH HOH . E 4 HOH A 48 104 104 HOH HOH . E 4 HOH A 49 106 106 HOH HOH . E 4 HOH A 50 110 110 HOH HOH . E 4 HOH A 51 111 111 HOH HOH . E 4 HOH A 52 113 113 HOH HOH . E 4 HOH A 53 115 115 HOH HOH . E 4 HOH A 54 118 118 HOH HOH . E 4 HOH A 55 119 119 HOH HOH . E 4 HOH A 56 120 120 HOH HOH . E 4 HOH A 57 122 122 HOH HOH . E 4 HOH A 58 123 123 HOH HOH . E 4 HOH A 59 124 124 HOH HOH . E 4 HOH A 60 125 125 HOH HOH . E 4 HOH A 61 126 126 HOH HOH . E 4 HOH A 62 127 127 HOH HOH . E 4 HOH A 63 130 130 HOH HOH . E 4 HOH A 64 131 131 HOH HOH . E 4 HOH A 65 135 135 HOH HOH . E 4 HOH A 66 137 137 HOH HOH . E 4 HOH A 67 142 142 HOH HOH . E 4 HOH A 68 150 150 HOH HOH . E 4 HOH A 69 155 155 HOH HOH . E 4 HOH A 70 158 158 HOH HOH . E 4 HOH A 71 159 159 HOH HOH . E 4 HOH A 72 160 160 HOH HOH . E 4 HOH A 73 161 161 HOH HOH . E 4 HOH A 74 162 162 HOH HOH . E 4 HOH A 75 166 166 HOH HOH . E 4 HOH A 76 168 168 HOH HOH . E 4 HOH A 77 170 170 HOH HOH . E 4 HOH A 78 172 172 HOH HOH . E 4 HOH A 79 173 173 HOH HOH . E 4 HOH A 80 174 174 HOH HOH . E 4 HOH A 81 175 175 HOH HOH . E 4 HOH A 82 182 182 HOH HOH . E 4 HOH A 83 183 183 HOH HOH . E 4 HOH A 84 185 185 HOH HOH . E 4 HOH A 85 186 186 HOH HOH . E 4 HOH A 86 188 25 HOH MO6 . E 4 HOH A 87 189 25 HOH MO6 . E 4 HOH A 88 191 25 HOH MO6 . F 4 HOH B 1 27 27 HOH HOH . F 4 HOH B 2 30 30 HOH HOH . F 4 HOH B 3 34 34 HOH HOH . F 4 HOH B 4 37 37 HOH HOH . F 4 HOH B 5 38 38 HOH HOH . F 4 HOH B 6 43 43 HOH HOH . F 4 HOH B 7 44 44 HOH HOH . F 4 HOH B 8 45 45 HOH HOH . F 4 HOH B 9 46 46 HOH HOH . F 4 HOH B 10 48 48 HOH HOH . F 4 HOH B 11 50 50 HOH HOH . F 4 HOH B 12 56 56 HOH HOH . F 4 HOH B 13 61 61 HOH HOH . F 4 HOH B 14 63 63 HOH HOH . F 4 HOH B 15 70 70 HOH HOH . F 4 HOH B 16 73 73 HOH HOH . F 4 HOH B 17 74 74 HOH HOH . F 4 HOH B 18 75 75 HOH HOH . F 4 HOH B 19 77 77 HOH HOH . F 4 HOH B 20 79 79 HOH HOH . F 4 HOH B 21 81 81 HOH HOH . F 4 HOH B 22 82 82 HOH HOH . F 4 HOH B 23 83 83 HOH HOH . F 4 HOH B 24 85 85 HOH HOH . F 4 HOH B 25 88 88 HOH HOH . F 4 HOH B 26 89 89 HOH HOH . F 4 HOH B 27 90 90 HOH HOH . F 4 HOH B 28 93 93 HOH HOH . F 4 HOH B 29 94 94 HOH HOH . F 4 HOH B 30 103 103 HOH HOH . F 4 HOH B 31 105 105 HOH HOH . F 4 HOH B 32 107 107 HOH HOH . F 4 HOH B 33 108 108 HOH HOH . F 4 HOH B 34 109 109 HOH HOH . F 4 HOH B 35 112 112 HOH HOH . F 4 HOH B 36 114 114 HOH HOH . F 4 HOH B 37 116 116 HOH HOH . F 4 HOH B 38 117 117 HOH HOH . F 4 HOH B 39 121 121 HOH HOH . F 4 HOH B 40 128 128 HOH HOH . F 4 HOH B 41 129 129 HOH HOH . F 4 HOH B 42 132 132 HOH HOH . F 4 HOH B 43 133 133 HOH HOH . F 4 HOH B 44 134 134 HOH HOH . F 4 HOH B 45 136 136 HOH HOH . F 4 HOH B 46 138 138 HOH HOH . F 4 HOH B 47 139 139 HOH HOH . F 4 HOH B 48 140 140 HOH HOH . F 4 HOH B 49 141 141 HOH HOH . F 4 HOH B 50 143 143 HOH HOH . F 4 HOH B 51 144 144 HOH HOH . F 4 HOH B 52 145 145 HOH HOH . F 4 HOH B 53 146 146 HOH HOH . F 4 HOH B 54 147 147 HOH HOH . F 4 HOH B 55 148 148 HOH HOH . F 4 HOH B 56 149 149 HOH HOH . F 4 HOH B 57 151 151 HOH HOH . F 4 HOH B 58 152 152 HOH HOH . F 4 HOH B 59 153 153 HOH HOH . F 4 HOH B 60 154 154 HOH HOH . F 4 HOH B 61 156 156 HOH HOH . F 4 HOH B 62 157 157 HOH HOH . F 4 HOH B 63 163 163 HOH HOH . F 4 HOH B 64 164 164 HOH HOH . F 4 HOH B 65 165 165 HOH HOH . F 4 HOH B 66 167 167 HOH HOH . F 4 HOH B 67 169 169 HOH HOH . F 4 HOH B 68 171 171 HOH HOH . F 4 HOH B 69 176 176 HOH HOH . F 4 HOH B 70 177 177 HOH HOH . F 4 HOH B 71 178 178 HOH HOH . F 4 HOH B 72 179 179 HOH HOH . F 4 HOH B 73 180 180 HOH HOH . F 4 HOH B 74 181 181 HOH HOH . F 4 HOH B 75 184 184 HOH HOH . F 4 HOH B 76 187 25 HOH MO6 . F 4 HOH B 77 190 25 HOH MO6 . F 4 HOH B 78 192 25 HOH MO6 . # 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 3.257 20.375 -2.961 1 23.13 ? N1 SPM 26 B 1 HETATM 2 C C2 SPM . . . D 3 4.594 20.448 -3.721 1 20.24 ? C2 SPM 26 B 1 HETATM 3 C C3 SPM . . . D 3 5.244 19.074 -3.822 1 19.51 ? C3 SPM 26 B 1 HETATM 4 C C4 SPM . . . D 3 6.466 19.082 -4.743 1 20.97 ? C4 SPM 26 B 1 HETATM 5 N N5 SPM . . . D 3 7.659 18.411 -4.078 1 21.48 ? N5 SPM 26 B 1 HETATM 6 C C6 SPM . . . D 3 8.387 17.46 -5.015 1 19.53 ? C6 SPM 26 B 1 HETATM 7 C C7 SPM . . . D 3 9.107 16.36 -4.239 1 16.81 ? C7 SPM 26 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 7 #