data_8PPX # _model_server_result.job_id -LacybqtEtrDsXnlacPLwg _model_server_result.datetime_utc '2025-01-18 05:21:06' _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 8ppx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":204}' # _entry.id 8PPX # _exptl.entry_id 8PPX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 286.24 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-oxidanyl-2-[4,5,7-tris(oxidanyl)naphthalen-2-yl]-1H-pyrimidin-6-one _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 8PPX _cell.length_a 73.96 _cell.length_b 73.96 _cell.length_c 128.18 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PPX _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 5 _struct_asym.id E _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 NE2 HIS 50 A HIS 41 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc2 A OE1 GLU 70 A GLU 80 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc3 A OD2 ASP 98 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc4 A OD1 ASP 98 A ASP 108 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc5 A OE2 GLU 109 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc6 A O ILE 110 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc7 B MN MN . A MN 201 1_555 E O1 85W . A 85W 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.805 ? metalc ? metalc8 B MN MN . A MN 201 1_555 E O5 85W . A 85W 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.799 ? metalc ? metalc9 C MG MG . A MG 202 1_555 E O1 85W . A 85W 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc10 C MG MG . A MG 202 1_555 F O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc11 C MG MG . A MG 202 1_555 F O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc12 C MG MG . A MG 202 1_555 F O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? # _chem_comp.formula 'C14 H10 N2 O5' _chem_comp.formula_weight 286.24 _chem_comp.id 85W _chem_comp.mon_nstd_flag . _chem_comp.name 5-oxidanyl-2-[4,5,7-tris(oxidanyl)naphthalen-2-yl]-1H-pyrimidin-6-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 5-oxidanyl-2-[4,5,7-tris(oxidanyl)naphthalen-2-yl]-1~{H}-pyrimidin-6-one # 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 85W sing 1 n n C1 C2 85W doub 2 n n C1 C14 85W sing 3 n n C2 N1 85W sing 4 n n O5 C14 85W doub 5 n n C14 N2 85W sing 6 n n N1 C3 85W doub 7 n n N2 C3 85W sing 8 n n C3 C4 85W sing 9 n n C13 C4 85W sing 10 n y C13 C12 85W doub 11 n y C4 C5 85W doub 12 n y O4 C12 85W sing 13 n n C12 C11 85W sing 14 n y C5 C6 85W sing 15 n y C11 C6 85W doub 16 n y C11 C10 85W sing 17 n y C6 C7 85W sing 18 n y O3 C10 85W sing 19 n n C10 C9 85W doub 20 n y C7 C8 85W doub 21 n y C9 C8 85W sing 22 n y C8 O2 85W sing 23 n n C5 H1 85W sing 24 n n C7 H2 85W sing 25 n n C13 H3 85W sing 26 n n O1 H4 85W sing 27 n n C2 H5 85W sing 28 n n O2 H6 85W sing 29 n n C9 H7 85W sing 30 n n O3 H8 85W sing 31 n n O4 H9 85W sing 32 n n N2 H10 85W sing 33 n n # _atom_sites.entry_id 8PPX _atom_sites.fract_transf_matrix[1][1] 0.013521 _atom_sites.fract_transf_matrix[1][2] 0.007806 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015613 _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] 0.007802 _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 B 2 MN A 1 201 1 MN MN . C 3 MG A 1 202 2 MG MG . D 4 CL A 1 203 1 CL CL . E 5 85W A 1 204 1 85W LIG . F 6 HOH A 1 301 12 HOH HOH . F 6 HOH A 2 302 27 HOH HOH . F 6 HOH A 3 303 2 HOH HOH . F 6 HOH A 4 304 29 HOH HOH . F 6 HOH A 5 305 1 HOH HOH . F 6 HOH A 6 306 22 HOH HOH . F 6 HOH A 7 307 15 HOH HOH . F 6 HOH A 8 308 28 HOH HOH . F 6 HOH A 9 309 24 HOH HOH . F 6 HOH A 10 310 13 HOH HOH . F 6 HOH A 11 311 3 HOH HOH . F 6 HOH A 12 312 23 HOH HOH . F 6 HOH A 13 313 7 HOH HOH . F 6 HOH A 14 314 16 HOH HOH . F 6 HOH A 15 315 30 HOH HOH . F 6 HOH A 16 316 25 HOH HOH . F 6 HOH A 17 317 31 HOH HOH . F 6 HOH A 18 318 10 HOH HOH . F 6 HOH A 19 319 11 HOH HOH . F 6 HOH A 20 320 6 HOH HOH . F 6 HOH A 21 321 17 HOH HOH . F 6 HOH A 22 322 14 HOH HOH . F 6 HOH A 23 323 5 HOH HOH . F 6 HOH A 24 324 19 HOH HOH . F 6 HOH A 25 325 18 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 85W . . . E 5 27.479 14.716 6.237 1 63.97 ? N1 85W 204 A 1 HETATM 2 C C4 85W . . . E 5 28.137 15.952 8.191 1 69.93 ? C4 85W 204 A 1 HETATM 3 C C5 85W . . . E 5 27.713 16.607 9.343 1 77.49 ? C5 85W 204 A 1 HETATM 4 C C6 85W . . . E 5 28.59 16.86 10.417 1 81.05 ? C6 85W 204 A 1 HETATM 5 C C7 85W . . . E 5 28.166 17.527 11.594 1 85.46 ? C7 85W 204 A 1 HETATM 6 C C8 85W . . . E 5 29.046 17.757 12.615 1 88.71 ? C8 85W 204 A 1 HETATM 7 C C10 85W . . . E 5 30.828 16.682 11.391 1 85.02 ? C10 85W 204 A 1 HETATM 8 C C13 85W . . . E 5 29.468 15.537 8.097 1 74.89 ? C13 85W 204 A 1 HETATM 9 O O1 85W . . . E 5 24.608 15.167 3.947 1 48.53 ? O1 85W 204 A 1 HETATM 10 C C1 85W . . . E 5 25.554 15.295 4.934 1 53.99 ? C1 85W 204 A 1 HETATM 11 C C2 85W . . . E 5 26.656 14.497 5.199 1 59.79 ? C2 85W 204 A 1 HETATM 12 C C3 85W . . . E 5 27.193 15.721 7.064 1 66.34 ? C3 85W 204 A 1 HETATM 13 O O2 85W . . . E 5 28.608 18.413 13.744 1 79.28 ? O2 85W 204 A 1 HETATM 14 C C9 85W . . . E 5 30.383 17.336 12.52 1 87.36 ? C9 85W 204 A 1 HETATM 15 O O3 85W . . . E 5 32.133 16.259 11.29 1 82.11 ? O3 85W 204 A 1 HETATM 16 C C11 85W . . . E 5 29.943 16.432 10.305 1 81.5 ? C11 85W 204 A 1 HETATM 17 C C12 85W . . . E 5 30.352 15.761 9.118 1 80.47 ? C12 85W 204 A 1 HETATM 18 O O4 85W . . . E 5 31.66 15.335 9.019 1 78.38 ? O4 85W 204 A 1 HETATM 19 N N2 85W . . . E 5 26.104 16.543 6.864 1 62.85 ? N2 85W 204 A 1 HETATM 20 C C14 85W . . . E 5 25.24 16.357 5.815 1 58.91 ? C14 85W 204 A 1 HETATM 21 O O5 85W . . . E 5 24.229 17.069 5.647 1 55.86 ? O5 85W 204 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #