data_5XJZ # _model_server_result.job_id huXSiMxc8mMgs_vKal7Psg _model_server_result.datetime_utc '2024-11-14 03:37:43' _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 5xjz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":101}' # _entry.id 5XJZ # _exptl.entry_id 5XJZ _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 5XJZ _cell.length_a 40.236 _cell.length_b 42.546 _cell.length_c 25.301 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XJZ _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 F _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 A N3 DC 4 A DC 4 1_555 E AG AG . A AG 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc2 A N7 DG 7 A DG 7 1_555 C AG AG . A AG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc3 A N3 DC 8 A DC 8 1_555 D AG AG . A AG 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc4 C AG AG . A AG 101 1_555 B N7 DG 7 B DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc5 D AG AG . A AG 102 1_555 B N3 DC 8 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc6 E AG AG . A AG 103 2_754 B N3 DC 4 B DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? hydrog 'DG-DC PAIR' hydrog1 A N2 DG 1 A DG 1 1_555 A O2 DC 6 A DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N1 DG 1 A DG 1 1_555 B N3 DC 6 B DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N2 DG 1 A DG 1 1_555 B O2 DC 6 B DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A O6 DG 1 A DG 1 1_555 B N4 DC 6 B DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog5 A O2 DC 2 A DC 2 1_555 A N2 DG 5 A DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 DC 2 A DC 2 1_555 B N1 DG 5 B DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N4 DC 2 A DC 2 1_555 B O6 DG 5 B DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O2 DC 2 A DC 2 1_555 B N2 DG 5 B DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_2_PAIR hydrog9 A N6 DA 3 A DA 3 1_555 B N7 DA 3 B DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_2_PAIR hydrog10 A N7 DA 3 A DA 3 1_555 B N6 DA 3 B DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N1 DG 5 A DG 5 1_555 B N3 DC 2 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N2 DG 5 A DG 5 1_555 B O2 DC 2 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O6 DG 5 A DG 5 1_555 B N4 DC 2 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N3 DC 6 A DC 6 1_555 B N1 DG 1 B DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N4 DC 6 A DC 6 1_555 B O6 DG 1 B DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O2 DC 6 A DC 6 1_555 B N2 DG 1 B DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog17 A O6 DG 7 A DG 7 1_555 B N4 DC 8 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog18 A N4 DC 8 A DC 8 1_555 B O6 DG 7 B DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog19 B N2 DG 1 B DG 1 1_555 B O2 DC 6 B DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog20 B O2 DC 2 B DC 2 1_555 B N2 DG 5 B DG 5 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 115 n n N1 HN11 SPM sing 116 n n N1 HN12 SPM sing 117 n n C2 C3 SPM sing 118 n n C2 H21 SPM sing 119 n n C2 H22 SPM sing 120 n n C3 C4 SPM sing 121 n n C3 H31 SPM sing 122 n n C3 H32 SPM sing 123 n n C4 N5 SPM sing 124 n n C4 H41 SPM sing 125 n n C4 H42 SPM sing 126 n n N5 C6 SPM sing 127 n n N5 HN5 SPM sing 128 n n C6 C7 SPM sing 129 n n C6 H61 SPM sing 130 n n C6 H62 SPM sing 131 n n C7 C8 SPM sing 132 n n C7 H71 SPM sing 133 n n C7 H72 SPM sing 134 n n C8 C9 SPM sing 135 n n C8 H81 SPM sing 136 n n C8 H82 SPM sing 137 n n C9 N10 SPM sing 138 n n C9 H91 SPM sing 139 n n C9 H92 SPM sing 140 n n N10 C11 SPM sing 141 n n N10 HN0 SPM sing 142 n n C11 C12 SPM sing 143 n n C11 H111 SPM sing 144 n n C11 H112 SPM sing 145 n n C12 C13 SPM sing 146 n n C12 H121 SPM sing 147 n n C12 H122 SPM sing 148 n n C13 N14 SPM sing 149 n n C13 H131 SPM sing 150 n n C13 H132 SPM sing 151 n n N14 HN41 SPM sing 152 n n N14 HN42 SPM sing 153 n n # _atom_sites.entry_id 5XJZ _atom_sites.fract_transf_matrix[1][1] 0.024853 _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] 0.023504 _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] 0.039524 _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 AG A 1 101 1 AG AG . D 2 AG A 1 102 2 AG AG . E 2 AG A 1 103 3 AG AG . F 3 SPM B 1 101 1 SPM SPM . G 4 HOH A 1 201 42 HOH HOH . G 4 HOH A 2 202 8 HOH HOH . G 4 HOH A 3 203 32 HOH HOH . G 4 HOH A 4 204 11 HOH HOH . G 4 HOH A 5 205 111 HOH HOH . G 4 HOH A 6 206 6 HOH HOH . G 4 HOH A 7 207 34 HOH HOH . G 4 HOH A 8 208 25 HOH HOH . G 4 HOH A 9 209 97 HOH HOH . G 4 HOH A 10 210 1 HOH HOH . G 4 HOH A 11 211 13 HOH HOH . G 4 HOH A 12 212 46 HOH HOH . G 4 HOH A 13 213 28 HOH HOH . G 4 HOH A 14 214 72 HOH HOH . G 4 HOH A 15 215 66 HOH HOH . G 4 HOH A 16 216 18 HOH HOH . G 4 HOH A 17 217 75 HOH HOH . G 4 HOH A 18 218 48 HOH HOH . G 4 HOH A 19 219 31 HOH HOH . G 4 HOH A 20 220 65 HOH HOH . G 4 HOH A 21 221 21 HOH HOH . G 4 HOH A 22 222 41 HOH HOH . G 4 HOH A 23 223 4 HOH HOH . G 4 HOH A 24 224 23 HOH HOH . G 4 HOH A 25 225 67 HOH HOH . G 4 HOH A 26 226 36 HOH HOH . G 4 HOH A 27 227 20 HOH HOH . G 4 HOH A 28 228 101 HOH HOH . G 4 HOH A 29 229 73 HOH HOH . G 4 HOH A 30 230 89 HOH HOH . G 4 HOH A 31 231 96 HOH HOH . G 4 HOH A 32 232 56 HOH HOH . G 4 HOH A 33 233 90 HOH HOH . G 4 HOH A 34 234 114 HOH HOH . G 4 HOH A 35 235 95 HOH HOH . G 4 HOH A 36 236 92 HOH HOH . G 4 HOH A 37 237 94 HOH HOH . G 4 HOH A 38 238 117 HOH HOH . G 4 HOH A 39 239 91 HOH HOH . G 4 HOH A 40 240 93 HOH HOH . H 4 HOH B 1 201 5 HOH HOH . H 4 HOH B 2 202 22 HOH HOH . H 4 HOH B 3 203 12 HOH HOH . H 4 HOH B 4 204 14 HOH HOH . H 4 HOH B 5 205 58 HOH HOH . H 4 HOH B 6 206 51 HOH HOH . H 4 HOH B 7 207 9 HOH HOH . H 4 HOH B 8 208 7 HOH HOH . H 4 HOH B 9 209 44 HOH HOH . H 4 HOH B 10 210 10 HOH HOH . H 4 HOH B 11 211 33 HOH HOH . H 4 HOH B 12 212 16 HOH HOH . H 4 HOH B 13 213 17 HOH HOH . H 4 HOH B 14 214 55 HOH HOH . H 4 HOH B 15 215 61 HOH HOH . H 4 HOH B 16 216 26 HOH HOH . H 4 HOH B 17 217 2 HOH HOH . H 4 HOH B 18 218 45 HOH HOH . H 4 HOH B 19 219 3 HOH HOH . H 4 HOH B 20 220 50 HOH HOH . H 4 HOH B 21 221 29 HOH HOH . H 4 HOH B 22 222 60 HOH HOH . H 4 HOH B 23 223 35 HOH HOH . H 4 HOH B 24 224 59 HOH HOH . H 4 HOH B 25 225 104 HOH HOH . H 4 HOH B 26 226 57 HOH HOH . H 4 HOH B 27 227 30 HOH HOH . H 4 HOH B 28 228 102 HOH HOH . H 4 HOH B 29 229 38 HOH HOH . H 4 HOH B 30 230 19 HOH HOH . H 4 HOH B 31 231 27 HOH HOH . H 4 HOH B 32 232 100 HOH HOH . H 4 HOH B 33 233 116 HOH HOH . H 4 HOH B 34 234 105 HOH HOH . H 4 HOH B 35 235 103 HOH HOH . H 4 HOH B 36 236 118 HOH HOH . H 4 HOH B 37 237 24 HOH HOH . H 4 HOH B 38 238 64 HOH HOH . H 4 HOH B 39 239 107 HOH HOH . H 4 HOH B 40 240 106 HOH HOH . H 4 HOH B 41 241 115 HOH HOH . H 4 HOH B 42 242 109 HOH HOH . H 4 HOH B 43 243 119 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 . . . F 3 24.943 1.688 -20.912 0.6 20.81 ? N1 SPM 101 B 1 HETATM 2 C C2 SPM . . . F 3 25.765 2.016 -19.741 0.6 20.52 ? C2 SPM 101 B 1 HETATM 3 C C3 SPM . . . F 3 27.068 2.678 -20.188 0.6 20.2 ? C3 SPM 101 B 1 HETATM 4 C C4 SPM . . . F 3 27.864 3.108 -18.954 0.6 20.1 ? C4 SPM 101 B 1 HETATM 5 N N5 SPM . . . F 3 29.139 3.69 -19.393 0.6 19.72 ? N5 SPM 101 B 1 HETATM 6 C C6 SPM . . . F 3 30.026 3.889 -18.232 0.6 19.84 ? C6 SPM 101 B 1 HETATM 7 C C7 SPM . . . F 3 31.18 4.771 -18.713 0.6 20.01 ? C7 SPM 101 B 1 HETATM 8 C C8 SPM . . . F 3 32.34 4.832 -17.712 1 19.32 ? C8 SPM 101 B 1 HETATM 9 C C9 SPM . . . F 3 33.595 4.948 -18.569 1 19.39 ? C9 SPM 101 B 1 HETATM 10 N N10 SPM . . . F 3 34.788 5.293 -17.795 1 19.39 ? N10 SPM 101 B 1 HETATM 11 C C11 SPM . . . F 3 35.92 5.102 -18.731 1 20.3 ? C11 SPM 101 B 1 HETATM 12 C C12 SPM . . . F 3 37.066 6.077 -18.485 1 20.67 ? C12 SPM 101 B 1 HETATM 13 C C13 SPM . . . F 3 36.806 7.471 -19.063 1 19.04 ? C13 SPM 101 B 1 HETATM 14 N N14 SPM . . . F 3 36.667 7.487 -20.527 1 18.17 ? N14 SPM 101 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #