data_4HIF # _model_server_result.job_id iVv5CHyQQl6t-PsE8KERqw _model_server_result.datetime_utc '2024-11-02 02:24:43' _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 4hif # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":103}' # _entry.id 4HIF # _exptl.entry_id 4HIF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 206.372 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SPERMINE (FULLY PROTONATED FORM)' _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 4HIF _cell.length_a 17.791 _cell.length_b 30.907 _cell.length_c 44.196 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HIF _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 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 4 _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 N7 DG 6 A DG 6 1_555 C ZN ZN . A ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc2 C ZN ZN . A ZN 101 1_555 G O HOH . A HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc3 C ZN ZN . A ZN 101 1_555 G O HOH . A HOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc4 C ZN ZN . A ZN 101 1_555 G O HOH . A HOH 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc5 C ZN ZN . A ZN 101 1_555 G O HOH . A HOH 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc6 C ZN ZN . A ZN 101 1_555 G O HOH . A HOH 235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc7 B N7 DG 4 B DG 10 1_555 D ZN ZN . B ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc8 D ZN ZN . B ZN 101 1_555 H O HOH . B HOH 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H30 N4 4' _chem_comp.formula_weight 206.372 _chem_comp.id SPK _chem_comp.mon_nstd_flag . _chem_comp.name 'SPERMINE (FULLY PROTONATED FORM)' _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 SPK sing 77 n n N1 H1A SPK sing 78 n n N1 H1B SPK sing 79 n n N1 H1C SPK sing 80 n n C2 C3 SPK sing 81 n n C2 H2A SPK sing 82 n n C2 H2B SPK sing 83 n n C3 C4 SPK sing 84 n n C3 H3A SPK sing 85 n n C3 H3B SPK sing 86 n n C4 N5 SPK sing 87 n n C4 H4A SPK sing 88 n n C4 H4B SPK sing 89 n n N5 C6 SPK sing 90 n n N5 H5A SPK sing 91 n n N5 H5B SPK sing 92 n n C6 C7 SPK sing 93 n n C6 H6A SPK sing 94 n n C6 H6B SPK sing 95 n n C7 C8 SPK sing 96 n n C7 H7A SPK sing 97 n n C7 H7B SPK sing 98 n n C8 C9 SPK sing 99 n n C8 H8A SPK sing 100 n n C8 H8B SPK sing 101 n n C9 N10 SPK sing 102 n n C9 H9A SPK sing 103 n n C9 H9B SPK sing 104 n n N10 C11 SPK sing 105 n n N10 H101 SPK sing 106 n n N10 H102 SPK sing 107 n n C11 C12 SPK sing 108 n n C11 H111 SPK sing 109 n n C11 H112 SPK sing 110 n n C12 C13 SPK sing 111 n n C12 H121 SPK sing 112 n n C12 H122 SPK sing 113 n n C13 N14 SPK sing 114 n n C13 H131 SPK sing 115 n n C13 H132 SPK sing 116 n n N14 H141 SPK sing 117 n n N14 H142 SPK sing 118 n n N14 H143 SPK sing 119 n n # _atom_sites.entry_id 4HIF _atom_sites.fract_transf_matrix[1][1] 0.056208 _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] 0.032355 _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] 0.022626 _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 ZN A 1 101 14 ZN ZN . D 2 ZN B 1 101 13 ZN ZN . E 3 CL B 1 102 15 CL CL . F 4 SPK B 1 103 16 SPK SPK . G 5 HOH A 1 201 21 HOH HOH . G 5 HOH A 2 202 24 HOH HOH . G 5 HOH A 3 203 25 HOH HOH . G 5 HOH A 4 204 27 HOH HOH . G 5 HOH A 5 205 28 HOH HOH . G 5 HOH A 6 206 30 HOH HOH . G 5 HOH A 7 207 32 HOH HOH . G 5 HOH A 8 208 33 HOH HOH . G 5 HOH A 9 209 35 HOH HOH . G 5 HOH A 10 210 42 HOH HOH . G 5 HOH A 11 211 44 HOH HOH . G 5 HOH A 12 212 45 HOH HOH . G 5 HOH A 13 213 46 HOH HOH . G 5 HOH A 14 214 47 HOH HOH . G 5 HOH A 15 215 48 HOH HOH . G 5 HOH A 16 216 50 HOH HOH . G 5 HOH A 17 217 52 HOH HOH . G 5 HOH A 18 218 53 HOH HOH . G 5 HOH A 19 219 54 HOH HOH . G 5 HOH A 20 220 59 HOH HOH . G 5 HOH A 21 221 60 HOH HOH . G 5 HOH A 22 222 61 HOH HOH . G 5 HOH A 23 223 68 HOH HOH . G 5 HOH A 24 224 69 HOH HOH . G 5 HOH A 25 225 70 HOH HOH . G 5 HOH A 26 226 71 HOH HOH . G 5 HOH A 27 227 72 HOH HOH . G 5 HOH A 28 228 73 HOH HOH . G 5 HOH A 29 229 74 HOH HOH . G 5 HOH A 30 230 76 HOH HOH . G 5 HOH A 31 231 79 HOH HOH . G 5 HOH A 32 232 80 HOH HOH . G 5 HOH A 33 233 81 HOH HOH . G 5 HOH A 34 234 82 HOH HOH . G 5 HOH A 35 235 83 HOH HOH . G 5 HOH A 36 236 87 HOH HOH . H 5 HOH B 1 201 17 HOH HOH . H 5 HOH B 2 202 18 HOH HOH . H 5 HOH B 3 203 19 HOH HOH . H 5 HOH B 4 204 20 HOH HOH . H 5 HOH B 5 205 22 HOH HOH . H 5 HOH B 6 206 23 HOH HOH . H 5 HOH B 7 207 26 HOH HOH . H 5 HOH B 8 208 29 HOH HOH . H 5 HOH B 9 209 31 HOH HOH . H 5 HOH B 10 210 34 HOH HOH . H 5 HOH B 11 211 36 HOH HOH . H 5 HOH B 12 212 37 HOH HOH . H 5 HOH B 13 213 38 HOH HOH . H 5 HOH B 14 214 39 HOH HOH . H 5 HOH B 15 215 40 HOH HOH . H 5 HOH B 16 216 41 HOH HOH . H 5 HOH B 17 217 43 HOH HOH . H 5 HOH B 18 218 49 HOH HOH . H 5 HOH B 19 219 51 HOH HOH . H 5 HOH B 20 220 55 HOH HOH . H 5 HOH B 21 221 56 HOH HOH . H 5 HOH B 22 222 57 HOH HOH . H 5 HOH B 23 223 58 HOH HOH . H 5 HOH B 24 224 62 HOH HOH . H 5 HOH B 25 225 63 HOH HOH . H 5 HOH B 26 226 64 HOH HOH . H 5 HOH B 27 227 65 HOH HOH . H 5 HOH B 28 228 66 HOH HOH . H 5 HOH B 29 229 67 HOH HOH . H 5 HOH B 30 230 75 HOH HOH . H 5 HOH B 31 231 77 HOH HOH . H 5 HOH B 32 232 78 HOH HOH . H 5 HOH B 33 233 84 HOH HOH . H 5 HOH B 34 234 85 HOH HOH . H 5 HOH B 35 235 86 HOH HOH . H 5 HOH B 36 236 88 HOH HOH . H 5 HOH B 37 237 89 HOH HOH . H 5 HOH B 38 238 90 HOH HOH . H 5 HOH B 39 239 91 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 SPK . . . F 4 10.672 23.301 34.004 0.83 6.39 ? N1 SPK 103 B 1 HETATM 2 C C2 SPK . . . F 4 9.97 22.358 34.937 1 8.93 ? C2 SPK 103 B 1 HETATM 3 C C3 SPK . . . F 4 8.471 22.631 34.848 0.82 12.47 ? C3 SPK 103 B 1 HETATM 4 C C4 SPK . . . F 4 7.614 21.512 35.544 0.89 17.14 ? C4 SPK 103 B 1 HETATM 5 N N5 SPK . . . F 4 7.812 21.952 36.921 0.6 10.59 ? N5 SPK 103 B 1 HETATM 6 C C6 SPK . . . F 4 6.713 21.319 37.704 0.4 8.24 ? C6 SPK 103 B 1 HETATM 7 C C7 SPK . . . F 4 6.772 21.657 39.176 0.22 5.58 ? C7 SPK 103 B 1 HETATM 8 C C8 SPK . . . F 4 8.146 21.338 39.756 0 15.38 ? C8 SPK 103 B 1 HETATM 9 C C9 SPK . . . F 4 8.341 22.131 41.041 0.34 20.69 ? C9 SPK 103 B 1 HETATM 10 N N10 SPK . . . F 4 9.497 21.693 41.828 0.51 18.56 ? N10 SPK 103 B 1 HETATM 11 C C11 SPK . . . F 4 9.91 22.636 42.872 0.79 26.4 ? C11 SPK 103 B 1 HETATM 12 C C12 SPK . . . F 4 8.704 23.158 43.693 0.19 34.25 ? C12 SPK 103 B 1 HETATM 13 C C13 SPK . . . F 4 9.02 24.364 44.579 1 39.56 ? C13 SPK 103 B 1 HETATM 14 N N14 SPK . . . F 4 9.162 25.522 43.675 0.76 17.53 ? N14 SPK 103 B 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #