data_1D63 # _model_server_result.job_id NNiYFj_1iSXyaTLpLuYbmw _model_server_result.datetime_utc '2024-11-30 04:35:37' _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 1d63 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":25}' # _entry.id 1D63 # _exptl.entry_id 1D63 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 281.316 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description BERENIL _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 1D63 _cell.length_a 24.64 _cell.length_b 40.61 _cell.length_c 65.07 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D63 _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,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 3 _struct_asym.id D _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 C MG MG . A MG 26 1_555 E O HOH . A HOH 41 3_657 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc2 C MG MG . A MG 26 1_555 E O HOH . A HOH 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc3 C MG MG . A MG 26 1_555 E O HOH . A HOH 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc4 C MG MG . A MG 26 1_555 E O HOH . A HOH 66 3_657 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc5 C MG MG . A MG 26 1_555 F O HOH . B HOH 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 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 DC 3 A DC 3 1_555 B N1 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DA 4 A DA 4 1_555 B N3 DT 9 B DT 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N6 DA 4 A DA 4 1_555 B O4 DT 9 B DT 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 DT 9 A DT 9 1_555 B N1 DA 4 B DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O4 DT 9 A DT 9 1_555 B N6 DA 4 B DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N1 DG 10 A DG 10 1_555 B N3 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N2 DG 10 A DG 10 1_555 B O2 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O6 DG 10 A DG 10 1_555 B N4 DC 3 B DC 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 'C14 H15 N7' _chem_comp.formula_weight 281.316 _chem_comp.id BRN _chem_comp.mon_nstd_flag . _chem_comp.name BERENIL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "DIMINAZINE ACETURATE;1,3-TRIS-(4'AMIDINOPHENYL)TRIAZINE" # 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 BRN doub 1 n y C1 C6 BRN sing 2 n y C1 N1 BRN sing 3 n n C2 C3 BRN sing 4 n y C2 H2 BRN sing 5 n n C3 C4 BRN doub 6 n y C3 H3 BRN sing 7 n n C4 C5 BRN sing 8 n y C4 C7 BRN sing 9 n n C5 C6 BRN doub 10 n y C5 H5 BRN sing 11 n n C6 H6 BRN sing 12 n n C7 NA BRN doub 13 n n C7 NB BRN sing 14 n n NA HA BRN sing 15 n n NB HB1 BRN sing 16 n n NB HB2 BRN sing 17 n n N1 N BRN sing 18 n n N1 HN1 BRN sing 19 n n N N1' BRN doub 20 e n N1' C1' BRN sing 21 n n C1' C2' BRN doub 22 n y C1' C6' BRN sing 23 n y C2' C3' BRN sing 24 n y C2' H2' BRN sing 25 n n C3' C4' BRN doub 26 n y C3' H3' BRN sing 27 n n C4' C5' BRN sing 28 n y C4' C7' BRN sing 29 n n C5' C6' BRN doub 30 n y C5' H5' BRN sing 31 n n C6' H6' BRN sing 32 n n C7' NA' BRN doub 33 n n C7' NB' BRN sing 34 n n NA' HA' BRN sing 35 n n NB' "HB'1" BRN sing 36 n n NB' "HB'2" BRN sing 37 n n # _atom_sites.entry_id 1D63 _atom_sites.fract_transf_matrix[1][1] 0.040584 _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] 0.024625 _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] 0.015368 _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 MG A 1 26 26 MG MG . D 3 BRN B 1 25 25 BRN BRN . E 4 HOH A 1 28 28 HOH HOH . E 4 HOH A 2 29 29 HOH HOH . E 4 HOH A 3 31 31 HOH HOH . E 4 HOH A 4 35 35 HOH HOH . E 4 HOH A 5 36 36 HOH HOH . E 4 HOH A 6 37 37 HOH HOH . E 4 HOH A 7 41 41 HOH HOH . E 4 HOH A 8 42 42 HOH HOH . E 4 HOH A 9 45 45 HOH HOH . E 4 HOH A 10 47 47 HOH HOH . E 4 HOH A 11 49 49 HOH HOH . E 4 HOH A 12 53 53 HOH HOH . E 4 HOH A 13 54 54 HOH HOH . E 4 HOH A 14 55 55 HOH HOH . E 4 HOH A 15 57 57 HOH HOH . E 4 HOH A 16 58 58 HOH HOH . E 4 HOH A 17 59 59 HOH HOH . E 4 HOH A 18 63 63 HOH HOH . E 4 HOH A 19 64 64 HOH HOH . E 4 HOH A 20 65 65 HOH HOH . E 4 HOH A 21 66 66 HOH HOH . E 4 HOH A 22 68 68 HOH HOH . E 4 HOH A 23 71 71 HOH HOH . E 4 HOH A 24 72 72 HOH HOH . E 4 HOH A 25 75 75 HOH HOH . E 4 HOH A 26 77 77 HOH HOH . E 4 HOH A 27 79 79 HOH HOH . E 4 HOH A 28 80 80 HOH HOH . E 4 HOH A 29 84 84 HOH HOH . E 4 HOH A 30 86 86 HOH HOH . E 4 HOH A 31 87 87 HOH HOH . E 4 HOH A 32 88 88 HOH HOH . E 4 HOH A 33 89 89 HOH HOH . E 4 HOH A 34 91 91 HOH HOH . F 4 HOH B 1 27 27 HOH HOH . F 4 HOH B 2 30 30 HOH HOH . F 4 HOH B 3 32 32 HOH HOH . F 4 HOH B 4 33 33 HOH HOH . F 4 HOH B 5 34 34 HOH HOH . F 4 HOH B 6 38 38 HOH HOH . F 4 HOH B 7 39 39 HOH HOH . F 4 HOH B 8 40 40 HOH HOH . F 4 HOH B 9 43 43 HOH HOH . F 4 HOH B 10 44 44 HOH HOH . F 4 HOH B 11 46 46 HOH HOH . F 4 HOH B 12 48 48 HOH HOH . F 4 HOH B 13 50 50 HOH HOH . F 4 HOH B 14 51 51 HOH HOH . F 4 HOH B 15 52 52 HOH HOH . F 4 HOH B 16 56 56 HOH HOH . F 4 HOH B 17 60 60 HOH HOH . F 4 HOH B 18 61 61 HOH HOH . F 4 HOH B 19 62 62 HOH HOH . F 4 HOH B 20 67 67 HOH HOH . F 4 HOH B 21 69 69 HOH HOH . F 4 HOH B 22 70 70 HOH HOH . F 4 HOH B 23 73 73 HOH HOH . F 4 HOH B 24 74 74 HOH HOH . F 4 HOH B 25 76 76 HOH HOH . F 4 HOH B 26 78 78 HOH HOH . F 4 HOH B 27 81 81 HOH HOH . F 4 HOH B 28 82 82 HOH HOH . F 4 HOH B 29 83 83 HOH HOH . F 4 HOH B 30 85 85 HOH HOH . F 4 HOH B 31 90 90 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 BRN . . . D 3 7.929 24.39 71.662 1 35.75 ? C1 BRN 25 B 1 HETATM 2 C C2 BRN . . . D 3 7.449 25.373 70.79 1 37.56 ? C2 BRN 25 B 1 HETATM 3 C C3 BRN . . . D 3 8.19 25.714 69.683 1 36.03 ? C3 BRN 25 B 1 HETATM 4 C C4 BRN . . . D 3 9.39 25.101 69.404 1 37 ? C4 BRN 25 B 1 HETATM 5 C C5 BRN . . . D 3 9.846 24.122 70.282 1 36.7 ? C5 BRN 25 B 1 HETATM 6 C C6 BRN . . . D 3 9.129 23.765 71.414 1 35.68 ? C6 BRN 25 B 1 HETATM 7 C C7 BRN . . . D 3 10.125 25.458 68.291 1 39.56 ? C7 BRN 25 B 1 HETATM 8 N NA BRN . . . D 3 11.118 24.626 67.822 1 38.86 ? NA BRN 25 B 1 HETATM 9 N NB BRN . . . D 3 9.959 26.725 67.757 1 39.64 ? NB BRN 25 B 1 HETATM 10 N N1 BRN . . . D 3 7.138 24.078 72.774 1 35.33 ? N1 BRN 25 B 1 HETATM 11 N N BRN . . . D 3 7.631 23.326 73.77 1 35.5 ? N BRN 25 B 1 HETATM 12 N N1' BRN . . . D 3 6.722 22.693 74.401 1 33.76 ? N1' BRN 25 B 1 HETATM 13 C C1' BRN . . . D 3 7.298 21.929 75.468 1 34.11 ? C1' BRN 25 B 1 HETATM 14 C C2' BRN . . . D 3 8.644 21.605 75.592 1 33.25 ? C2' BRN 25 B 1 HETATM 15 C C3' BRN . . . D 3 9.063 20.894 76.685 1 31.58 ? C3' BRN 25 B 1 HETATM 16 C C4' BRN . . . D 3 8.161 20.467 77.648 1 31.92 ? C4' BRN 25 B 1 HETATM 17 C C5' BRN . . . D 3 6.83 20.792 77.524 1 32.9 ? C5' BRN 25 B 1 HETATM 18 C C6' BRN . . . D 3 6.389 21.531 76.431 1 34.69 ? C6' BRN 25 B 1 HETATM 19 C C7' BRN . . . D 3 8.57 19.732 78.735 1 33.06 ? C7' BRN 25 B 1 HETATM 20 N NA' BRN . . . D 3 9.923 19.578 78.988 1 32.17 ? NA' BRN 25 B 1 HETATM 21 N NB' BRN . . . D 3 7.658 18.92 79.398 1 29.32 ? NB' BRN 25 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 194 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 21 #