data_8OEX # _model_server_result.job_id c-e1EmqSMgfjQHNeIRbJbA _model_server_result.datetime_utc '2025-01-10 10:55:38' _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 8oex # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 8OEX # _exptl.entry_id 8OEX _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 8OEX _cell.length_a 18.283 _cell.length_b 30.764 _cell.length_c 42.477 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OEX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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 _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 N3 DC 1 A DC 1 1_555 B N1 DG 6 B DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 6 B DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 6 B DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 5 B DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 5 B DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 5 B DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 4 B DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 4 B DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 4 B DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 3 B DC 3 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N1 DG 4 A DG 4 1_555 B N3 DC 3 B DC 3 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N2 DG 4 A DG 4 1_555 B O2 DC 3 B DC 3 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N2 DG 4 A DG 4 1_555 B O2 DC 3 B DC 3 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O6 DG 4 A DG 4 1_555 B N4 DC 3 B DC 3 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O6 DG 4 A DG 4 1_555 B N4 DC 3 B DC 3 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 2 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 2 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 2 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 2 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 2 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 2 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 1 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 1 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 1 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 1 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 1 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 1 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? # _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 77 n n N1 HN11 SPM sing 78 n n N1 HN12 SPM sing 79 n n C2 C3 SPM sing 80 n n C2 H21 SPM sing 81 n n C2 H22 SPM sing 82 n n C3 C4 SPM sing 83 n n C3 H31 SPM sing 84 n n C3 H32 SPM sing 85 n n C4 N5 SPM sing 86 n n C4 H41 SPM sing 87 n n C4 H42 SPM sing 88 n n N5 C6 SPM sing 89 n n N5 HN5 SPM sing 90 n n C6 C7 SPM sing 91 n n C6 H61 SPM sing 92 n n C6 H62 SPM sing 93 n n C7 C8 SPM sing 94 n n C7 H71 SPM sing 95 n n C7 H72 SPM sing 96 n n C8 C9 SPM sing 97 n n C8 H81 SPM sing 98 n n C8 H82 SPM sing 99 n n C9 N10 SPM sing 100 n n C9 H91 SPM sing 101 n n C9 H92 SPM sing 102 n n N10 C11 SPM sing 103 n n N10 HN0 SPM sing 104 n n C11 C12 SPM sing 105 n n C11 H111 SPM sing 106 n n C11 H112 SPM sing 107 n n C12 C13 SPM sing 108 n n C12 H121 SPM sing 109 n n C12 H122 SPM sing 110 n n C13 N14 SPM sing 111 n n C13 H131 SPM sing 112 n n C13 H132 SPM sing 113 n n N14 HN41 SPM sing 114 n n N14 HN42 SPM sing 115 n n # _atom_sites.entry_id 8OEX _atom_sites.fract_transf_matrix[1][1] 0.054696 _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] 0.032506 _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] 0.023542 _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 1 101 101 SPM SPM . D 3 HOH A 1 201 80 HOH HOH . D 3 HOH A 2 202 56 HOH HOH . D 3 HOH A 3 203 25 HOH HOH . D 3 HOH A 4 204 57 HOH HOH . D 3 HOH A 5 205 13 HOH HOH . D 3 HOH A 6 206 1 HOH HOH . D 3 HOH A 7 207 30 HOH HOH . D 3 HOH A 8 208 64 HOH HOH . D 3 HOH A 9 209 14 HOH HOH . D 3 HOH A 10 210 31 HOH HOH . D 3 HOH A 11 211 2 HOH HOH . D 3 HOH A 12 212 23 HOH HOH . D 3 HOH A 13 213 92 HOH HOH . D 3 HOH A 14 214 18 HOH HOH . D 3 HOH A 15 215 58 HOH HOH . D 3 HOH A 16 216 83 HOH HOH . D 3 HOH A 17 217 32 HOH HOH . D 3 HOH A 18 218 34 HOH HOH . D 3 HOH A 19 219 6 HOH HOH . D 3 HOH A 20 220 27 HOH HOH . D 3 HOH A 21 221 9 HOH HOH . D 3 HOH A 22 222 3 HOH HOH . D 3 HOH A 23 223 79 HOH HOH . D 3 HOH A 24 224 12 HOH HOH . D 3 HOH A 25 225 10 HOH HOH . D 3 HOH A 26 226 85 HOH HOH . D 3 HOH A 27 227 48 HOH HOH . D 3 HOH A 28 228 29 HOH HOH . D 3 HOH A 29 229 93 HOH HOH . D 3 HOH A 30 230 60 HOH HOH . D 3 HOH A 31 231 49 HOH HOH . D 3 HOH A 32 232 61 HOH HOH . D 3 HOH A 33 233 90 HOH HOH . D 3 HOH A 34 234 19 HOH HOH . D 3 HOH A 35 235 22 HOH HOH . D 3 HOH A 36 236 73 HOH HOH . D 3 HOH A 37 237 76 HOH HOH . D 3 HOH A 38 238 72 HOH HOH . D 3 HOH A 39 239 15 HOH HOH . D 3 HOH A 40 240 86 HOH HOH . D 3 HOH A 41 241 47 HOH HOH . D 3 HOH A 42 242 51 HOH HOH . D 3 HOH A 43 243 53 HOH HOH . D 3 HOH A 44 244 68 HOH HOH . D 3 HOH A 45 245 70 HOH HOH . D 3 HOH A 46 246 54 HOH HOH . D 3 HOH A 47 247 33 HOH HOH . D 3 HOH A 48 248 74 HOH HOH . D 3 HOH A 49 249 67 HOH HOH . D 3 HOH A 50 250 46 HOH HOH . D 3 HOH A 51 251 55 HOH HOH . D 3 HOH A 52 252 71 HOH HOH . D 3 HOH A 53 253 81 HOH HOH . E 3 HOH B 1 101 62 HOH HOH . E 3 HOH B 2 102 45 HOH HOH . E 3 HOH B 3 103 37 HOH HOH . E 3 HOH B 4 104 65 HOH HOH . E 3 HOH B 5 105 11 HOH HOH . E 3 HOH B 6 106 91 HOH HOH . E 3 HOH B 7 107 21 HOH HOH . E 3 HOH B 8 108 20 HOH HOH . E 3 HOH B 9 109 4 HOH HOH . E 3 HOH B 10 110 40 HOH HOH . E 3 HOH B 11 111 16 HOH HOH . E 3 HOH B 12 112 36 HOH HOH . E 3 HOH B 13 113 38 HOH HOH . E 3 HOH B 14 114 5 HOH HOH . E 3 HOH B 15 115 43 HOH HOH . E 3 HOH B 16 116 59 HOH HOH . E 3 HOH B 17 117 69 HOH HOH . E 3 HOH B 18 118 7 HOH HOH . E 3 HOH B 19 119 8 HOH HOH . E 3 HOH B 20 120 75 HOH HOH . E 3 HOH B 21 121 24 HOH HOH . E 3 HOH B 22 122 52 HOH HOH . E 3 HOH B 23 123 35 HOH HOH . E 3 HOH B 24 124 28 HOH HOH . E 3 HOH B 25 125 17 HOH HOH . E 3 HOH B 26 126 87 HOH HOH . E 3 HOH B 27 127 82 HOH HOH . E 3 HOH B 28 128 39 HOH HOH . E 3 HOH B 29 129 42 HOH HOH . E 3 HOH B 30 130 78 HOH HOH . E 3 HOH B 31 131 66 HOH HOH . E 3 HOH B 32 132 50 HOH HOH . E 3 HOH B 33 133 44 HOH HOH . E 3 HOH B 34 134 77 HOH HOH . E 3 HOH B 35 135 63 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 -5.315 3.05 -5.577 1 3.49 ? N1 SPM 101 A 1 HETATM 2 C C2 SPM . . . C 2 -5.172 1.681 -5.039 1 3.85 ? C2 SPM 101 A 1 HETATM 3 C C3 SPM . . . C 2 -3.964 1.592 -4.12 1 4.01 ? C3 SPM 101 A 1 HETATM 4 C C4 SPM . . . C 2 -3.722 0.174 -3.588 1 3.97 ? C4 SPM 101 A 1 HETATM 5 N N5 SPM . . . C 2 -4.754 -0.33 -2.674 1 4.22 ? N5 SPM 101 A 1 HETATM 6 C C6 SPM . . . C 2 -4.261 -1.504 -1.927 1 4.7 ? C6 SPM 101 A 1 HETATM 7 C C7 SPM . . . C 2 -5.342 -2.128 -1.038 1 5.58 ? C7 SPM 101 A 1 HETATM 8 C C8 SPM . . . C 2 -4.752 -3.123 -0.022 1 5.63 ? C8 SPM 101 A 1 HETATM 9 C C9 SPM . . . C 2 -5.856 -3.689 0.876 1 6.2 ? C9 SPM 101 A 1 HETATM 10 N N10 SPM . . . C 2 -5.344 -4.631 1.891 1 6.43 ? N10 SPM 101 A 1 HETATM 11 C C11 SPM . . . C 2 -6.379 -4.999 2.883 1 7.3 ? C11 SPM 101 A 1 HETATM 12 C C12 SPM . . . C 2 -5.923 -6.112 3.852 1 7.4 ? C12 SPM 101 A 1 HETATM 13 C C13 SPM . . . C 2 -7.076 -6.521 4.789 1 7.85 ? C13 SPM 101 A 1 HETATM 14 N N14 SPM . . . C 2 -6.695 -7.592 5.712 1 7.3 ? N14 SPM 101 A 1 HETATM 15 H HN11 SPM . . . C 2 -6.008 3.079 -6.135 1 4.18 ? HN11 SPM 101 A 1 HETATM 16 H HN12 SPM . . . C 2 -5.45 3.62 -4.907 1 4.18 ? HN12 SPM 101 A 1 HETATM 17 H H21 SPM . . . C 2 -5.061 1.058 -5.774 1 4.62 ? H21 SPM 101 A 1 HETATM 18 H H22 SPM . . . C 2 -5.971 1.448 -4.541 1 4.62 ? H22 SPM 101 A 1 HETATM 19 H H31 SPM . . . C 2 -4.1 2.189 -3.367 1 4.81 ? H31 SPM 101 A 1 HETATM 20 H H32 SPM . . . C 2 -3.178 1.88 -4.609 1 4.81 ? H32 SPM 101 A 1 HETATM 21 H H41 SPM . . . C 2 -2.871 0.164 -3.123 1 4.76 ? H41 SPM 101 A 1 HETATM 22 H H42 SPM . . . C 2 -3.664 -0.43 -4.345 1 4.76 ? H42 SPM 101 A 1 HETATM 23 H H61 SPM . . . C 2 -3.516 -1.233 -1.369 1 5.64 ? H61 SPM 101 A 1 HETATM 24 H H62 SPM . . . C 2 -3.952 -2.171 -2.56 1 5.64 ? H62 SPM 101 A 1 HETATM 25 H H71 SPM . . . C 2 -5.977 -2.596 -1.601 1 6.69 ? H71 SPM 101 A 1 HETATM 26 H H72 SPM . . . C 2 -5.804 -1.422 -0.559 1 6.69 ? H72 SPM 101 A 1 HETATM 27 H H81 SPM . . . C 2 -4.323 -3.851 -0.499 1 6.76 ? H81 SPM 101 A 1 HETATM 28 H H82 SPM . . . C 2 -4.095 -2.668 0.527 1 6.76 ? H82 SPM 101 A 1 HETATM 29 H H91 SPM . . . C 2 -6.299 -2.954 1.328 1 7.44 ? H91 SPM 101 A 1 HETATM 30 H H92 SPM . . . C 2 -6.504 -4.15 0.321 1 7.44 ? H92 SPM 101 A 1 HETATM 31 H H111 SPM . . . C 2 -6.609 -4.211 3.4 1 8.76 ? H111 SPM 101 A 1 HETATM 32 H H112 SPM . . . C 2 -7.169 -5.303 2.41 1 8.76 ? H112 SPM 101 A 1 HETATM 33 H H121 SPM . . . C 2 -5.179 -5.788 4.384 1 8.88 ? H121 SPM 101 A 1 HETATM 34 H H122 SPM . . . C 2 -5.637 -6.885 3.34 1 8.88 ? H122 SPM 101 A 1 HETATM 35 H H131 SPM . . . C 2 -7.35 -5.746 5.304 1 9.41 ? H131 SPM 101 A 1 HETATM 36 H H132 SPM . . . C 2 -7.825 -6.821 4.252 1 9.41 ? H132 SPM 101 A 1 HETATM 37 H HN41 SPM . . . C 2 -6.514 -8.331 5.25 1 8.76 ? HN41 SPM 101 A 1 HETATM 38 H HN42 SPM . . . C 2 -7.366 -7.751 6.275 1 8.76 ? HN42 SPM 101 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 38 #