data_4MNB # _model_server_result.job_id Sp7tr29Dnp5pBn0xEj5akg _model_server_result.datetime_utc '2024-10-17 23:58:42' _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 4mnb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 4MNB # _exptl.entry_id 4MNB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 293.283 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "9-amino-5-(2-aminopyrimidin-4-yl)pyrido[3',2':4,5]pyrrolo[1,2-c]pyrimidin-4-ol" _entity.pdbx_number_of_molecules 2 _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 4MNB _cell.length_a 28.7 _cell.length_b 53.4 _cell.length_c 40.8 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4MNB _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 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,G,H,I,J,K _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N 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 2 A DG 2 1_555 E CO NCO . A NCO 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc2 B N7 DG 2 B DG 8 1_555 H CO NCO . B NCO 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc3 B OP2 DG 2 B DG 8 1_555 I NA NA . B NA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc4 B N7 DG 6 B DG 12 1_555 G CO NCO . B NCO 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? hydrog WATSON-CRICK hydrog1 A N1 DG 2 A DG 2 1_555 B N3 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 2 A DG 2 1_555 B O2 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 2 A DG 2 1_555 B N4 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DT 3 A DT 3 1_555 B N1 DA 4 B DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O4 DT 3 A DT 3 1_555 B N6 DA 4 B DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DA 4 A DA 4 1_555 B N3 DT 3 B DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 DA 4 A DA 4 1_555 B O4 DT 3 B DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C14 H11 N7 O' _chem_comp.formula_weight 293.283 _chem_comp.id VAR _chem_comp.mon_nstd_flag . _chem_comp.name "9-amino-5-(2-aminopyrimidin-4-yl)pyrido[3',2':4,5]pyrrolo[1,2-c]pyrimidin-4-ol" _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 O1 C1 VAR sing 176 n n C1 C2 VAR sing 177 n y C1 C10 VAR doub 178 n y C2 C3 VAR doub 179 n y C3 N1 VAR sing 180 n y N1 C4 VAR doub 181 n y C4 N2 VAR sing 182 n y C4 C10 VAR sing 183 n y N2 C5 VAR sing 184 n y N2 C8 VAR sing 185 n y C5 N3 VAR sing 186 n n C5 N4 VAR doub 187 n y N4 C6 VAR sing 188 n y C6 C7 VAR doub 189 n y C7 C8 VAR sing 190 n y C8 C9 VAR doub 191 n y C9 C10 VAR sing 192 n y C9 C11 VAR sing 193 n y C11 C14 VAR sing 194 n y C11 N5 VAR doub 195 n y C14 C13 VAR doub 196 n y C13 N7 VAR sing 197 n y N7 C12 VAR doub 198 n y C12 N5 VAR sing 199 n y C12 N6 VAR sing 200 n n O1 HO1 VAR sing 201 n n C2 H2 VAR sing 202 n n C3 H3 VAR sing 203 n n N3 HN3 VAR sing 204 n n N3 HN3A VAR sing 205 n n C6 H6 VAR sing 206 n n C7 H7 VAR sing 207 n n C14 H14 VAR sing 208 n n C13 H13 VAR sing 209 n n N6 HN6 VAR sing 210 n n N6 HN6A VAR sing 211 n n # _atom_sites.entry_id 4MNB _atom_sites.fract_transf_matrix[1][1] 0.034843 _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] 0.018727 _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] 0.02451 _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 VAR A 1 101 1 VAR VAR . D 2 VAR A 1 102 1 VAR VAR . E 3 NCO A 1 103 1 NCO NCO . F 4 CO A 1 104 1 CO CO . G 3 NCO B 1 101 1 NCO NCO . H 3 NCO B 1 102 1 NCO NCO . I 5 NA B 1 103 1 NA NA . J 6 HOH A 1 201 2 HOH HOH . J 6 HOH A 2 202 3 HOH HOH . J 6 HOH A 3 203 6 HOH HOH . J 6 HOH A 4 204 8 HOH HOH . J 6 HOH A 5 205 9 HOH HOH . J 6 HOH A 6 206 12 HOH HOH . J 6 HOH A 7 207 14 HOH HOH . J 6 HOH A 8 208 15 HOH HOH . J 6 HOH A 9 209 16 HOH HOH . J 6 HOH A 10 210 17 HOH HOH . J 6 HOH A 11 211 18 HOH HOH . J 6 HOH A 12 212 23 HOH HOH . J 6 HOH A 13 213 24 HOH HOH . K 6 HOH B 1 201 1 HOH HOH . K 6 HOH B 2 202 4 HOH HOH . K 6 HOH B 3 203 5 HOH HOH . K 6 HOH B 4 204 7 HOH HOH . K 6 HOH B 5 205 10 HOH HOH . K 6 HOH B 6 206 11 HOH HOH . K 6 HOH B 7 207 13 HOH HOH . K 6 HOH B 8 208 19 HOH HOH . K 6 HOH B 9 209 20 HOH HOH . K 6 HOH B 10 210 21 HOH HOH . K 6 HOH B 11 211 22 HOH HOH . K 6 HOH B 12 212 25 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 O O1 VAR . . . C 2 17.349 -3.931 -5.702 0.5 33.1 ? O1 VAR 101 A 1 HETATM 2 C C1 VAR . . . C 2 18.332 -4.566 -6.406 0.5 26.08 ? C1 VAR 101 A 1 HETATM 3 C C2 VAR . . . C 2 19.098 -5.571 -5.796 0.5 27.27 ? C2 VAR 101 A 1 HETATM 4 C C3 VAR . . . C 2 20.124 -6.225 -6.466 0.5 28.6 ? C3 VAR 101 A 1 HETATM 5 N N1 VAR . . . C 2 20.381 -5.869 -7.729 0.5 27.01 ? N1 VAR 101 A 1 HETATM 6 C C4 VAR . . . C 2 19.613 -4.904 -8.312 0.5 23.05 ? C4 VAR 101 A 1 HETATM 7 N N2 VAR . . . C 2 19.822 -4.545 -9.543 0.5 22.9 ? N2 VAR 101 A 1 HETATM 8 C C5 VAR . . . C 2 20.806 -5.127 -10.258 0.5 22.11 ? C5 VAR 101 A 1 HETATM 9 N N3 VAR . . . C 2 21.563 -6.11 -9.715 0.5 24.62 ? N3 VAR 101 A 1 HETATM 10 N N4 VAR . . . C 2 20.997 -4.739 -11.532 0.5 23.47 ? N4 VAR 101 A 1 HETATM 11 C C6 VAR . . . C 2 20.157 -3.742 -11.964 0.5 25.32 ? C6 VAR 101 A 1 HETATM 12 C C7 VAR . . . C 2 19.114 -3.127 -11.171 0.5 23.76 ? C7 VAR 101 A 1 HETATM 13 C C8 VAR . . . C 2 18.937 -3.581 -9.866 0.5 21.5 ? C8 VAR 101 A 1 HETATM 14 C C9 VAR . . . C 2 18.072 -3.264 -8.749 0.5 21.24 ? C9 VAR 101 A 1 HETATM 15 C C10 VAR . . . C 2 18.606 -4.199 -7.696 0.5 23.74 ? C10 VAR 101 A 1 HETATM 16 C C11 VAR . . . C 2 16.925 -2.31 -8.433 0.5 16.63 ? C11 VAR 101 A 1 HETATM 17 C C14 VAR . . . C 2 16.215 -1.549 -9.379 0.5 16.96 ? C14 VAR 101 A 1 HETATM 18 C C13 VAR . . . C 2 15.185 -0.704 -8.897 0.5 17.02 ? C13 VAR 101 A 1 HETATM 19 N N7 VAR . . . C 2 14.895 -0.6 -7.603 0.5 17.73 ? N7 VAR 101 A 1 HETATM 20 C C12 VAR . . . C 2 15.556 -1.299 -6.666 0.5 17.97 ? C12 VAR 101 A 1 HETATM 21 N N5 VAR . . . C 2 16.559 -2.145 -7.1 0.5 18.21 ? N5 VAR 101 A 1 HETATM 22 N N6 VAR . . . C 2 15.167 -1.13 -5.349 0.5 19.28 ? N6 VAR 101 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 22 #