data_3EY0 # _model_server_result.job_id HSEWCYtzeSGYjxAaInq-tw _model_server_result.datetime_utc '2024-12-02 16:20:54' _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 3ey0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":11}' # _entry.id 3EY0 # _exptl.entry_id 3EY0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 340.419 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,5-BIS(4-AMIDINOPHENOXY)PENTANE _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 120 _cell.entry_id 3EY0 _cell.length_a 27.789 _cell.length_b 27.789 _cell.length_c 311.95 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EY0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 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 _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 E O HOH . A HOH 27 1_555 D MG MG . B MG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc2 E O HOH . A HOH 28 1_555 D MG MG . B MG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc3 E O HOH . A HOH 29 1_555 D MG MG . B MG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc4 D MG MG . B MG 11 1_555 F O HOH . B HOH 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc5 D MG MG . B MG 11 1_555 F O HOH . B HOH 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc6 D MG MG . B MG 11 1_555 F O HOH . B HOH 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? hydrog WATSON-CRICK hydrog1 A N1 DA 1 A DA 1 1_555 B N3 DT 10 B DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N6 DA 1 A DA 1 1_555 B O4 DT 10 B DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N3 DT 2 A DT 2 1_555 B N1 DA 9 B DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A O4 DT 2 A DT 2 1_555 B N6 DA 9 B DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N1 DA 3 A DA 3 1_555 B N3 DT 8 B DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N6 DA 3 A DA 3 1_555 B O4 DT 8 B DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DT 4 A DT 4 1_555 B N1 DA 7 B DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O4 DT 4 A DT 4 1_555 B N6 DA 7 B DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 DA 5 A DA 5 1_555 B N3 DT 6 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N6 DA 5 A DA 5 1_555 B O4 DT 6 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 DT 6 A DT 6 1_555 B N1 DA 5 B DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O4 DT 6 A DT 6 1_555 B N6 DA 5 B DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DA 7 A DA 7 1_555 B N3 DT 4 B DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 DA 7 A DA 7 1_555 B O4 DT 4 B DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 DT 8 A DT 8 1_555 B N1 DA 3 B DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O4 DT 8 A DT 8 1_555 B N6 DA 3 B DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 DA 9 A DA 9 1_555 B N3 DT 2 B DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N6 DA 9 A DA 9 1_555 B O4 DT 2 B DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog HOOGSTEEN hydrog19 A N3 DT 10 A DT 10 1_555 B N7 DA 1 B DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog HOOGSTEEN hydrog20 A O4 DT 10 A DT 10 1_555 B N6 DA 1 B DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C19 H24 N4 O2' _chem_comp.formula_weight 340.419 _chem_comp.id PNT _chem_comp.mon_nstd_flag . _chem_comp.name 1,5-BIS(4-AMIDINOPHENOXY)PENTANE _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 C1 C2 PNT doub 78 n y C1 C6 PNT sing 79 n y C1 O1 PNT sing 80 n n C2 C3 PNT sing 81 n y C2 H2 PNT sing 82 n n C3 C4 PNT doub 83 n y C3 H3 PNT sing 84 n n C4 C5 PNT sing 85 n y C4 C9 PNT sing 86 n n C5 C6 PNT doub 87 n y C5 H5 PNT sing 88 n n C6 H6 PNT sing 89 n n C7 C8 PNT sing 90 n n C7 O1 PNT sing 91 n n C7 H71 PNT sing 92 n n C7 H72 PNT sing 93 n n C8 C10 PNT sing 94 n n C8 H81 PNT sing 95 n n C8 H82 PNT sing 96 n n C9 N1 PNT doub 97 n n C9 N2 PNT sing 98 n n C10 C8' PNT sing 99 n n C10 H101 PNT sing 100 n n C10 H102 PNT sing 101 n n C1' C2' PNT doub 102 n y C1' C6' PNT sing 103 n y C1' O1' PNT sing 104 n n C2' C3' PNT sing 105 n y C2' H2' PNT sing 106 n n C3' C4' PNT doub 107 n y C3' H3' PNT sing 108 n n C4' C5' PNT sing 109 n y C4' C9' PNT sing 110 n n C5' C6' PNT doub 111 n y C5' H5' PNT sing 112 n n C6' H6' PNT sing 113 n n C7' C8' PNT sing 114 n n C7' O1' PNT sing 115 n n C7' "H7'1" PNT sing 116 n n C7' "H7'2" PNT sing 117 n n C8' "H8'1" PNT sing 118 n n C8' "H8'2" PNT sing 119 n n C9' N1' PNT doub 120 n n C9' N2' PNT sing 121 n n N1 HN1 PNT sing 122 n n N2 HN2 PNT sing 123 n n N2 HN3 PNT sing 124 n n N1' "HN'1" PNT sing 125 n n N2' "HN'2" PNT sing 126 n n N2' "HN'3" PNT sing 127 n n # _atom_sites.entry_id 3EY0 _atom_sites.fract_transf_matrix[1][1] 0.035985 _atom_sites.fract_transf_matrix[1][2] 0.020776 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.041552 _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] 0.003206 _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 PNT A 1 11 1 PNT PNT . D 3 MG B 1 11 1 MG MG . E 4 HOH A 1 12 4 HOH HOH . E 4 HOH A 2 13 5 HOH HOH . E 4 HOH A 3 14 9 HOH HOH . E 4 HOH A 4 15 11 HOH HOH . E 4 HOH A 5 16 13 HOH HOH . E 4 HOH A 6 17 15 HOH HOH . E 4 HOH A 7 18 17 HOH HOH . E 4 HOH A 8 19 18 HOH HOH . E 4 HOH A 9 20 19 HOH HOH . E 4 HOH A 10 21 29 HOH HOH . E 4 HOH A 11 22 35 HOH HOH . E 4 HOH A 12 23 41 HOH HOH . E 4 HOH A 13 24 43 HOH HOH . E 4 HOH A 14 25 57 HOH HOH . E 4 HOH A 15 26 58 HOH HOH . E 4 HOH A 16 27 66 HOH HOH . E 4 HOH A 17 28 67 HOH HOH . E 4 HOH A 18 29 68 HOH HOH . E 4 HOH A 19 30 70 HOH HOH . E 4 HOH A 20 32 79 HOH HOH . E 4 HOH A 21 33 80 HOH HOH . E 4 HOH A 22 34 81 HOH HOH . E 4 HOH A 23 35 82 HOH HOH . E 4 HOH A 24 36 83 HOH HOH . E 4 HOH A 25 37 84 HOH HOH . E 4 HOH A 26 38 86 HOH HOH . E 4 HOH A 27 39 87 HOH HOH . F 4 HOH B 1 31 77 HOH HOH . F 4 HOH B 2 32 1 HOH HOH . F 4 HOH B 3 33 2 HOH HOH . F 4 HOH B 4 34 3 HOH HOH . F 4 HOH B 5 35 7 HOH HOH . F 4 HOH B 6 36 12 HOH HOH . F 4 HOH B 7 37 14 HOH HOH . F 4 HOH B 8 38 22 HOH HOH . F 4 HOH B 9 39 25 HOH HOH . F 4 HOH B 10 40 27 HOH HOH . F 4 HOH B 11 41 28 HOH HOH . F 4 HOH B 12 42 30 HOH HOH . F 4 HOH B 13 43 31 HOH HOH . F 4 HOH B 14 44 59 HOH HOH . F 4 HOH B 15 45 60 HOH HOH . F 4 HOH B 16 46 61 HOH HOH . F 4 HOH B 17 47 63 HOH HOH . F 4 HOH B 18 48 64 HOH HOH . F 4 HOH B 19 49 71 HOH HOH . F 4 HOH B 20 50 72 HOH HOH . F 4 HOH B 21 51 73 HOH HOH . F 4 HOH B 22 52 74 HOH HOH . F 4 HOH B 23 53 78 HOH HOH . F 4 HOH B 24 54 88 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 C C1 PNT . . . C 2 11.509 15.587 88.612 1 55.04 ? C1 PNT 11 A 1 HETATM 2 C C2 PNT . . . C 2 11.278 14.264 89.012 1 42.6 ? C2 PNT 11 A 1 HETATM 3 C C3 PNT . . . C 2 10.012 13.714 88.883 1 48.78 ? C3 PNT 11 A 1 HETATM 4 C C4 PNT . . . C 2 8.971 14.485 88.357 1 51.98 ? C4 PNT 11 A 1 HETATM 5 C C5 PNT . . . C 2 9.204 15.798 87.946 1 52.29 ? C5 PNT 11 A 1 HETATM 6 C C6 PNT . . . C 2 10.47 16.349 88.067 1 54.74 ? C6 PNT 11 A 1 HETATM 7 C C7 PNT . . . C 2 13.902 15.418 89.125 1 57.02 ? C7 PNT 11 A 1 HETATM 8 C C8 PNT . . . C 2 15.15 16.247 88.902 1 50.75 ? C8 PNT 11 A 1 HETATM 9 C C9 PNT . . . C 2 7.604 13.89 88.238 1 52.58 ? C9 PNT 11 A 1 HETATM 10 C C10 PNT . . . C 2 16.349 15.458 89.394 1 49.55 ? C10 PNT 11 A 1 HETATM 11 C C1' PNT . . . C 2 20.98 16.084 90.734 1 56.77 ? C1' PNT 11 A 1 HETATM 12 C C2' PNT . . . C 2 21.297 14.747 90.499 1 49.06 ? C2' PNT 11 A 1 HETATM 13 C C3' PNT . . . C 2 22.562 14.277 90.806 1 46.53 ? C3' PNT 11 A 1 HETATM 14 C C4' PNT . . . C 2 23.524 15.125 91.345 1 47.66 ? C4' PNT 11 A 1 HETATM 15 C C5' PNT . . . C 2 23.196 16.46 91.573 1 43.74 ? C5' PNT 11 A 1 HETATM 16 C C6' PNT . . . C 2 21.932 16.937 91.271 1 53.82 ? C6' PNT 11 A 1 HETATM 17 C C7' PNT . . . C 2 18.705 15.7 90.012 1 61.68 ? C7' PNT 11 A 1 HETATM 18 C C8' PNT . . . C 2 17.359 16.403 90.02 1 43.93 ? C8' PNT 11 A 1 HETATM 19 C C9' PNT . . . C 2 24.913 14.622 91.673 1 50.06 ? C9' PNT 11 A 1 HETATM 20 O O1 PNT . . . C 2 12.754 16.163 88.725 1 53.73 ? O1 PNT 11 A 1 HETATM 21 O O1' PNT . . . C 2 19.736 16.581 90.447 1 47.36 ? O1' PNT 11 A 1 HETATM 22 N N1 PNT . . . C 2 7.34 12.8 88.825 1 43.82 ? N1 PNT 11 A 1 HETATM 23 N N2 PNT . . . C 2 6.659 14.522 87.539 1 60.03 ? N2 PNT 11 A 1 HETATM 24 N N1' PNT . . . C 2 25.373 13.546 91.195 1 34.97 ? N1' PNT 11 A 1 HETATM 25 N N2' PNT . . . C 2 25.696 15.336 92.468 1 44.77 ? N2' PNT 11 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 455 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #