data_5T4W # _model_server_result.job_id K4uZq0gAq2yhZ7as0GNvEQ _model_server_result.datetime_utc '2025-07-14 08:19:51' _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 5t4w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 5T4W # _exptl.entry_id 5T4W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 277.324 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE _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 5T4W _cell.length_a 24.503 _cell.length_b 41.09 _cell.length_c 65.184 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5T4W _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 _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 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DT 3 A DT 3 1_555 B N1 DA 10 B DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O4 DT 3 A DT 3 1_555 B N6 DA 10 B DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 DG 4 A DG 4 1_555 B N3 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N2 DG 4 A DG 4 1_555 B O2 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O6 DG 4 A DG 4 1_555 B N4 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 DA 5 A DA 5 1_555 B N3 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N6 DA 5 A DA 5 1_555 B O4 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 DA 6 A DA 6 1_555 B N3 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N6 DA 6 A DA 6 1_555 B O4 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 DT 7 A DT 7 1_555 B N1 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O4 DT 7 A DT 7 1_555 B N6 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N3 DT 8 A DT 8 1_555 B N1 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O4 DT 8 A DT 8 1_555 B N6 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N3 DC 9 A DC 9 1_555 B N1 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N4 DC 9 A DC 9 1_555 B O6 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O2 DC 9 A DC 9 1_555 B N2 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 DA 10 A DA 10 1_555 B N3 DT 3 B DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N6 DA 10 A DA 10 1_555 B O4 DT 3 B DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N3 DC 11 A DC 11 1_555 B N1 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N4 DC 11 A DC 11 1_555 B O6 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O2 DC 11 A DC 11 1_555 B N2 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N1 DG 12 A DG 12 1_555 B N3 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N2 DG 12 A DG 12 1_555 B O2 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A O6 DG 12 A DG 12 1_555 B N4 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C16 H15 N5' _chem_comp.formula_weight 277.324 _chem_comp.id DAP _chem_comp.mon_nstd_flag . _chem_comp.name 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE _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 DAP sing 39 n y N1 C8 DAP sing 40 n y N1 HN1 DAP sing 41 n n C2 C3 DAP doub 42 n y C2 C1' DAP sing 43 n y C3 C9 DAP sing 44 n y C3 H3 DAP sing 45 n n C4 C5 DAP doub 46 n y C4 C9 DAP sing 47 n y C4 H4 DAP sing 48 n n C5 C6 DAP sing 49 n y C5 H5 DAP sing 50 n n C6 C7 DAP doub 51 n y C6 C10 DAP sing 52 n n C7 C8 DAP sing 53 n y C7 H7 DAP sing 54 n n C8 C9 DAP doub 55 n y C10 N2 DAP doub 56 n n C10 N3 DAP sing 57 n n N2 HN2 DAP sing 58 n n N3 HN31 DAP sing 59 n n N3 HN32 DAP sing 60 n n C1' C2' DAP doub 61 n y C1' C6' DAP sing 62 n y C2' C3' DAP sing 63 n y C2' H2' DAP sing 64 n n C3' C4' DAP doub 65 n y C3' H3' DAP sing 66 n n C4' C5' DAP sing 67 n y C4' C11 DAP sing 68 n n C5' C6' DAP doub 69 n y C5' H5' DAP sing 70 n n C6' H6' DAP sing 71 n n C11 N4 DAP doub 72 n n C11 N5 DAP sing 73 n n N4 HN4 DAP sing 74 n n N5 HN51 DAP sing 75 n n N5 HN52 DAP sing 76 n n # _atom_sites.entry_id 5T4W _atom_sites.fract_transf_matrix[1][1] 0.040811 _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] 0.024337 _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] 0.015341 _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 DAP A 1 101 1 DAP DAP . D 3 HOH A 1 201 1 HOH HOH . D 3 HOH A 2 202 3 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 DAP . . . C 2 45.902 43.217 9.512 1 39.37 ? N1 DAP 101 A 1 HETATM 2 C C2 DAP . . . C 2 44.963 43.934 8.78 1 36.01 ? C2 DAP 101 A 1 HETATM 3 C C3 DAP . . . C 2 43.724 43.722 9.331 1 41.1 ? C3 DAP 101 A 1 HETATM 4 C C4 DAP . . . C 2 43.094 42.256 11.429 1 41.7 ? C4 DAP 101 A 1 HETATM 5 C C5 DAP . . . C 2 43.608 41.446 12.435 1 44.8 ? C5 DAP 101 A 1 HETATM 6 C C6 DAP . . . C 2 44.979 41.168 12.517 1 42.61 ? C6 DAP 101 A 1 HETATM 7 C C7 DAP . . . C 2 45.816 41.731 11.533 1 38.1 ? C7 DAP 101 A 1 HETATM 8 C C8 DAP . . . C 2 45.28 42.555 10.524 1 40.6 ? C8 DAP 101 A 1 HETATM 9 C C9 DAP . . . C 2 43.907 42.827 10.462 1 41.69 ? C9 DAP 101 A 1 HETATM 10 C C10 DAP . . . C 2 45.472 40.271 13.588 1 45.49 ? C10 DAP 101 A 1 HETATM 11 N N2 DAP . . . C 2 46.79 40.226 13.862 1 44.37 ? N2 DAP 101 A 1 HETATM 12 N N3 DAP . . . C 2 44.754 39.508 14.297 1 48.37 ? N3 DAP 101 A 1 HETATM 13 C C1' DAP . . . C 2 45.386 44.695 7.58 1 36.39 ? C1' DAP 101 A 1 HETATM 14 C C2' DAP . . . C 2 44.595 45.711 7.01 1 39.09 ? C2' DAP 101 A 1 HETATM 15 C C3' DAP . . . C 2 45.049 46.383 5.865 1 41.26 ? C3' DAP 101 A 1 HETATM 16 C C4' DAP . . . C 2 46.283 46.033 5.287 1 41.83 ? C4' DAP 101 A 1 HETATM 17 C C5' DAP . . . C 2 47.02 45.025 5.868 1 40.39 ? C5' DAP 101 A 1 HETATM 18 C C6' DAP . . . C 2 46.577 44.381 6.981 1 38.41 ? C6' DAP 101 A 1 HETATM 19 C C11 DAP . . . C 2 46.824 46.709 4.09 1 40.77 ? C11 DAP 101 A 1 HETATM 20 N N4 DAP . . . C 2 47.829 46.204 3.465 1 37.11 ? N4 DAP 101 A 1 HETATM 21 N N5 DAP . . . C 2 46.298 47.881 3.694 1 44.05 ? N5 DAP 101 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #