data_8OEB # _model_server_result.job_id UXiyI4dbLw3GJ1tdADpkkw _model_server_result.datetime_utc '2024-10-10 10:28:56' _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 8oeb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 8OEB # _exptl.entry_id 8OEB _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 8OEB _cell.length_a 18.312 _cell.length_b 30.78 _cell.length_c 43.159 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OEB _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,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 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 metalc ? metalc1 A N7 DG 2 A DG 2 1_555 F CU CU . A CU 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc2 A N7 DG 4 A DG 4 1_555 D CU CU . A CU 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc3 A N7 DG 6 A DG 6 1_555 E CU CU . A CU 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc4 C N5 SPM . A SPM 101 1_555 D CU CU . A CU 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 1 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 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 8OEB _atom_sites.fract_transf_matrix[1][1] 0.054609 _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] 0.032489 _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] 0.02317 _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 CU A 1 102 1 CU CU . E 3 CU A 1 103 2 CU CU . F 3 CU A 1 104 3 CU CU . G 4 HOH A 1 201 14 HOH HOH . G 4 HOH A 2 202 9 HOH HOH . G 4 HOH A 3 203 17 HOH HOH . G 4 HOH A 4 204 12 HOH HOH . G 4 HOH A 5 205 32 HOH HOH . G 4 HOH A 6 206 30 HOH HOH . G 4 HOH A 7 207 2 HOH HOH . G 4 HOH A 8 208 18 HOH HOH . G 4 HOH A 9 209 11 HOH HOH . G 4 HOH A 10 210 20 HOH HOH . G 4 HOH A 11 211 6 HOH HOH . G 4 HOH A 12 212 33 HOH HOH . G 4 HOH A 13 213 31 HOH HOH . H 4 HOH B 1 101 15 HOH HOH . H 4 HOH B 2 102 23 HOH HOH . H 4 HOH B 3 103 22 HOH HOH . H 4 HOH B 4 104 21 HOH HOH . H 4 HOH B 5 105 24 HOH HOH . H 4 HOH B 6 106 3 HOH HOH . H 4 HOH B 7 107 16 HOH HOH . H 4 HOH B 8 108 10 HOH HOH . H 4 HOH B 9 109 27 HOH HOH . H 4 HOH B 10 110 28 HOH HOH . H 4 HOH B 11 111 26 HOH HOH . H 4 HOH B 12 112 8 HOH HOH . H 4 HOH B 13 113 13 HOH HOH . H 4 HOH B 14 114 19 HOH HOH . H 4 HOH B 15 115 25 HOH HOH . H 4 HOH B 16 116 29 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 -5.496 3.076 -5.697 1 13.35 ? N1 SPM 101 A 1 HETATM 2 C C2 SPM . . . C 2 -5.361 1.744 -5.05 1 20.19 ? C2 SPM 101 A 1 HETATM 3 C C3 SPM . . . C 2 -4.196 1.768 -4.063 1 17.52 ? C3 SPM 101 A 1 HETATM 4 C C4 SPM . . . C 2 -3.84 0.346 -3.599 1 20.27 ? C4 SPM 101 A 1 HETATM 5 N N5 SPM . . . C 2 -4.972 -0.25 -2.875 1 15.98 ? N5 SPM 101 A 1 HETATM 6 C C6 SPM . . . C 2 -4.526 -1.523 -2.291 1 21.2 ? C6 SPM 101 A 1 HETATM 7 C C7 SPM . . . C 2 -5.455 -1.96 -1.168 1 24.97 ? C7 SPM 101 A 1 HETATM 8 C C8 SPM . . . C 2 -4.795 -3.06 -0.325 1 17.13 ? C8 SPM 101 A 1 HETATM 9 C C9 SPM . . . C 2 -5.585 -3.308 0.967 1 33.91 ? C9 SPM 101 A 1 HETATM 10 N N10 SPM . . . C 2 -5.271 -4.623 1.534 1 26.59 ? N10 SPM 101 A 1 HETATM 11 C C11 SPM . . . C 2 -6.301 -5.009 2.488 1 39.85 ? C11 SPM 101 A 1 HETATM 12 C C12 SPM . . . C 2 -5.838 -4.73 3.915 1 52.01 ? C12 SPM 101 A 1 HETATM 13 C C13 SPM . . . C 2 -5.183 -5.986 4.466 1 35.64 ? C13 SPM 101 A 1 HETATM 14 N N14 SPM . . . C 2 -6.197 -6.937 4.929 1 41.9 ? N14 SPM 101 A 1 HETATM 15 H HN11 SPM . . . C 2 -5.677 3.689 -5.078 1 16.03 ? HN11 SPM 101 A 1 HETATM 16 H HN12 SPM . . . C 2 -6.157 3.051 -6.293 1 16.03 ? HN12 SPM 101 A 1 HETATM 17 H H21 SPM . . . C 2 -6.18 1.53 -4.577 1 24.24 ? H21 SPM 101 A 1 HETATM 18 H H22 SPM . . . C 2 -5.195 1.071 -5.729 1 24.24 ? H22 SPM 101 A 1 HETATM 19 H H31 SPM . . . C 2 -4.439 2.307 -3.296 1 21.04 ? H31 SPM 101 A 1 HETATM 20 H H32 SPM . . . C 2 -3.423 2.163 -4.495 1 21.04 ? H32 SPM 101 A 1 HETATM 21 H H41 SPM . . . C 2 -3.631 -0.2 -4.373 1 24.34 ? H41 SPM 101 A 1 HETATM 22 H H42 SPM . . . C 2 -3.065 0.388 -3.019 1 24.34 ? H42 SPM 101 A 1 HETATM 23 H H61 SPM . . . C 2 -4.519 -2.204 -2.981 1 25.45 ? H61 SPM 101 A 1 HETATM 24 H H62 SPM . . . C 2 -3.629 -1.42 -1.937 1 25.45 ? H62 SPM 101 A 1 HETATM 25 H H71 SPM . . . C 2 -6.276 -2.304 -1.55 1 29.97 ? H71 SPM 101 A 1 HETATM 26 H H72 SPM . . . C 2 -5.66 -1.198 -0.605 1 29.97 ? H72 SPM 101 A 1 HETATM 27 H H81 SPM . . . C 2 -3.891 -2.79 -0.098 1 20.56 ? H81 SPM 101 A 1 HETATM 28 H H82 SPM . . . C 2 -4.762 -3.881 -0.841 1 20.56 ? H82 SPM 101 A 1 HETATM 29 H H91 SPM . . . C 2 -6.531 -3.254 0.76 1 40.7 ? H91 SPM 101 A 1 HETATM 30 H H92 SPM . . . C 2 -5.362 -2.623 1.616 1 40.7 ? H92 SPM 101 A 1 HETATM 31 H H111 SPM . . . C 2 -7.105 -4.493 2.324 1 47.83 ? H111 SPM 101 A 1 HETATM 32 H H112 SPM . . . C 2 -6.523 -5.94 2.416 1 47.83 ? H112 SPM 101 A 1 HETATM 33 H H121 SPM . . . C 2 -5.197 -4.002 3.913 1 62.42 ? H121 SPM 101 A 1 HETATM 34 H H122 SPM . . . C 2 -6.601 -4.492 4.465 1 62.42 ? H122 SPM 101 A 1 HETATM 35 H H131 SPM . . . C 2 -4.601 -5.749 5.205 1 42.78 ? H131 SPM 101 A 1 HETATM 36 H H132 SPM . . . C 2 -4.658 -6.393 3.76 1 42.78 ? H132 SPM 101 A 1 HETATM 37 H HN41 SPM . . . C 2 -5.801 -7.691 5.187 1 50.28 ? HN41 SPM 101 A 1 HETATM 38 H HN42 SPM . . . C 2 -6.642 -6.586 5.615 1 50.28 ? 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 234 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #