data_323D # _model_server_result.job_id so4lw37c4Jp0PnPjylyH2w _model_server_result.datetime_utc '2024-10-18 14:25:36' _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 323d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":21}' # _entry.id 323D # _exptl.entry_id 323D _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 323D _cell.length_a 24.78 _cell.length_b 44.57 _cell.length_c 48 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 323D _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 _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 covale ? covale1 A O3' DC 7 A DC 7 1_555 A P 5CM 8 A 5CM 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? covale ? covale2 A O3' 5CM 8 A 5CM 8 1_555 A P DG 9 A DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.596 ? covale ? covale3 B O3' DC 7 B DC 17 1_555 B P 5CM 8 B 5CM 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.622 ? covale ? covale4 B O3' 5CM 8 B 5CM 18 1_555 B P DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.625 ? hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 10 B DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 10 B DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 10 B DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DC 2 A DC 2 1_555 B N1 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 DC 2 A DC 2 1_555 B O6 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 DC 2 A DC 2 1_555 B N2 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DG 3 A DG 3 1_555 B N3 5CM 8 B 5CM 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 DG 3 A DG 3 1_555 B O2 5CM 8 B 5CM 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 DG 3 A DG 3 1_555 B N4 5CM 8 B 5CM 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 7 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 7 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 7 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DG 5 A DG 5 1_555 B N3 DC 6 B DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N2 DG 5 A DG 5 1_555 B O2 DC 6 B DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O6 DG 5 A DG 5 1_555 B N4 DC 6 B DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 DC 6 A DC 6 1_555 B N1 DG 5 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 DC 6 A DC 6 1_555 B O6 DG 5 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 DC 6 A DC 6 1_555 B N2 DG 5 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N3 DC 7 A DC 7 1_555 B N1 DG 4 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N4 DC 7 A DC 7 1_555 B O6 DG 4 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O2 DC 7 A DC 7 1_555 B N2 DG 4 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N3 5CM 8 A 5CM 8 1_555 B N1 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N4 5CM 8 A 5CM 8 1_555 B O6 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O2 5CM 8 A 5CM 8 1_555 B N2 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N1 DG 9 A DG 9 1_555 B N3 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N2 DG 9 A DG 9 1_555 B O2 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O6 DG 9 A DG 9 1_555 B N4 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N1 DG 10 A DG 10 1_555 B N3 DC 1 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N2 DG 10 A DG 10 1_555 B O2 DC 1 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A O6 DG 10 A DG 10 1_555 B N4 DC 1 B DC 11 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 323D _atom_sites.fract_transf_matrix[1][1] 0.040355 _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] 0.022437 _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] 0.020833 _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 B 1 21 21 SPM SPM . D 3 HOH A 1 22 22 HOH HOH . D 3 HOH A 2 23 23 HOH HOH . D 3 HOH A 3 25 25 HOH HOH . D 3 HOH A 4 28 28 HOH HOH . D 3 HOH A 5 29 29 HOH HOH . D 3 HOH A 6 30 30 HOH HOH . D 3 HOH A 7 32 32 HOH HOH . D 3 HOH A 8 34 34 HOH HOH . D 3 HOH A 9 35 35 HOH HOH . D 3 HOH A 10 37 37 HOH HOH . D 3 HOH A 11 38 38 HOH HOH . D 3 HOH A 12 39 39 HOH HOH . D 3 HOH A 13 41 41 HOH HOH . D 3 HOH A 14 44 44 HOH HOH . D 3 HOH A 15 45 45 HOH HOH . D 3 HOH A 16 48 48 HOH HOH . D 3 HOH A 17 49 49 HOH HOH . D 3 HOH A 18 50 50 HOH HOH . D 3 HOH A 19 51 51 HOH HOH . D 3 HOH A 20 52 52 HOH HOH . D 3 HOH A 21 54 54 HOH HOH . D 3 HOH A 22 55 55 HOH HOH . D 3 HOH A 23 56 56 HOH HOH . D 3 HOH A 24 57 57 HOH HOH . D 3 HOH A 25 58 58 HOH HOH . D 3 HOH A 26 59 59 HOH HOH . D 3 HOH A 27 60 60 HOH HOH . D 3 HOH A 28 61 61 HOH HOH . D 3 HOH A 29 62 62 HOH HOH . D 3 HOH A 30 63 63 HOH HOH . D 3 HOH A 31 64 64 HOH HOH . D 3 HOH A 32 70 70 HOH HOH . D 3 HOH A 33 85 85 HOH HOH . D 3 HOH A 34 86 86 HOH HOH . D 3 HOH A 35 87 87 HOH HOH . D 3 HOH A 36 88 88 HOH HOH . D 3 HOH A 37 90 90 HOH HOH . D 3 HOH A 38 92 92 HOH HOH . D 3 HOH A 39 93 93 HOH HOH . D 3 HOH A 40 94 94 HOH HOH . D 3 HOH A 41 95 95 HOH HOH . D 3 HOH A 42 96 96 HOH HOH . D 3 HOH A 43 97 97 HOH HOH . D 3 HOH A 44 98 98 HOH HOH . D 3 HOH A 45 99 99 HOH HOH . D 3 HOH A 46 100 100 HOH HOH . D 3 HOH A 47 101 101 HOH HOH . D 3 HOH A 48 102 102 HOH HOH . D 3 HOH A 49 103 103 HOH HOH . D 3 HOH A 50 104 104 HOH HOH . D 3 HOH A 51 109 109 HOH HOH . D 3 HOH A 52 112 112 HOH HOH . D 3 HOH A 53 113 113 HOH HOH . D 3 HOH A 54 114 114 HOH HOH . D 3 HOH A 55 115 115 HOH HOH . D 3 HOH A 56 116 116 HOH HOH . D 3 HOH A 57 117 117 HOH HOH . D 3 HOH A 58 118 118 HOH HOH . D 3 HOH A 59 119 119 HOH HOH . D 3 HOH A 60 120 120 HOH HOH . D 3 HOH A 61 121 121 HOH HOH . E 3 HOH B 1 24 24 HOH HOH . E 3 HOH B 2 26 26 HOH HOH . E 3 HOH B 3 27 27 HOH HOH . E 3 HOH B 4 31 31 HOH HOH . E 3 HOH B 5 33 33 HOH HOH . E 3 HOH B 6 36 36 HOH HOH . E 3 HOH B 7 40 40 HOH HOH . E 3 HOH B 8 42 42 HOH HOH . E 3 HOH B 9 43 43 HOH HOH . E 3 HOH B 10 46 46 HOH HOH . E 3 HOH B 11 47 47 HOH HOH . E 3 HOH B 12 53 53 HOH HOH . E 3 HOH B 13 65 65 HOH HOH . E 3 HOH B 14 66 66 HOH HOH . E 3 HOH B 15 67 67 HOH HOH . E 3 HOH B 16 68 68 HOH HOH . E 3 HOH B 17 69 69 HOH HOH . E 3 HOH B 18 71 71 HOH HOH . E 3 HOH B 19 72 72 HOH HOH . E 3 HOH B 20 73 73 HOH HOH . E 3 HOH B 21 74 74 HOH HOH . E 3 HOH B 22 75 75 HOH HOH . E 3 HOH B 23 76 76 HOH HOH . E 3 HOH B 24 77 77 HOH HOH . E 3 HOH B 25 78 78 HOH HOH . E 3 HOH B 26 79 79 HOH HOH . E 3 HOH B 27 80 80 HOH HOH . E 3 HOH B 28 81 81 HOH HOH . E 3 HOH B 29 82 82 HOH HOH . E 3 HOH B 30 83 83 HOH HOH . E 3 HOH B 31 84 84 HOH HOH . E 3 HOH B 32 89 89 HOH HOH . E 3 HOH B 33 91 91 HOH HOH . E 3 HOH B 34 105 105 HOH HOH . E 3 HOH B 35 106 106 HOH HOH . E 3 HOH B 36 107 107 HOH HOH . E 3 HOH B 37 108 108 HOH HOH . E 3 HOH B 38 110 110 HOH HOH . E 3 HOH B 39 111 111 HOH HOH . E 3 HOH B 40 122 122 HOH HOH . E 3 HOH B 41 123 123 HOH HOH . E 3 HOH B 42 124 124 HOH HOH . E 3 HOH B 43 125 125 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 -4.622 9.476 29.192 1 48.61 ? N1 SPM 21 B 1 HETATM 2 C C2 SPM . . . C 2 -5.276 9.424 27.903 1 48.7 ? C2 SPM 21 B 1 HETATM 3 C C3 SPM . . . C 2 -6.468 8.517 28.037 1 45.17 ? C3 SPM 21 B 1 HETATM 4 C C4 SPM . . . C 2 -7.346 8.54 26.812 1 41.6 ? C4 SPM 21 B 1 HETATM 5 N N5 SPM . . . C 2 -8.101 7.309 26.81 1 43.4 ? N5 SPM 21 B 1 HETATM 6 C C6 SPM . . . C 2 -8.675 7.137 25.503 1 42.72 ? C6 SPM 21 B 1 HETATM 7 C C7 SPM . . . C 2 -8.44 5.735 24.978 1 46.19 ? C7 SPM 21 B 1 HETATM 8 C C8 SPM . . . C 2 -9.027 5.782 23.586 1 50.1 ? C8 SPM 21 B 1 HETATM 9 C C9 SPM . . . C 2 -8.158 5.067 22.575 1 50.92 ? C9 SPM 21 B 1 HETATM 10 N N10 SPM . . . C 2 -8.089 5.905 21.395 1 47.05 ? N10 SPM 21 B 1 HETATM 11 C C11 SPM . . . C 2 -7.363 5.224 20.352 1 46.79 ? C11 SPM 21 B 1 HETATM 12 C C12 SPM . . . C 2 -7.349 6.079 19.102 1 45.03 ? C12 SPM 21 B 1 HETATM 13 C C13 SPM . . . C 2 -6.827 5.185 17.996 1 44.19 ? C13 SPM 21 B 1 HETATM 14 N N14 SPM . . . C 2 -6.842 5.854 16.716 1 48.24 ? N14 SPM 21 B 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #