data_7CA8 # _model_server_result.job_id XyfV8Eh23fOjtN1YWhQA6A _model_server_result.datetime_utc '2024-11-21 10:27:14' _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 7ca8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 7CA8 # _exptl.entry_id 7CA8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 288.295 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione _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 7CA8 _cell.length_a 67.96 _cell.length_b 102.37 _cell.length_c 103.54 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7CA8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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,E _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 # _chem_comp.formula 'C16 H16 O5' _chem_comp.formula_weight 288.295 _chem_comp.id FNO _chem_comp.mon_nstd_flag . _chem_comp.name 2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms shikonin # 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 C21 C17 FNO sing 83 n n C17 C20 FNO sing 84 n n C17 C14 FNO doub 85 n n C14 C08 FNO sing 86 n n C06 O01 FNO sing 87 n n C06 C08 FNO sing 88 n n C06 C07 FNO sing 89 n n C12 C07 FNO doub 90 n n C12 C13 FNO sing 91 n n C07 C10 FNO sing 92 n n O04 C13 FNO doub 93 n n C13 C11 FNO sing 94 n n C10 O02 FNO doub 95 n n C10 C09 FNO sing 96 n n C11 C09 FNO doub 97 n y C11 C16 FNO sing 98 n y C09 C15 FNO sing 99 n y O05 C16 FNO sing 100 n n C16 C19 FNO doub 101 n y C15 O03 FNO sing 102 n n C15 C18 FNO doub 103 n y C19 C18 FNO sing 104 n y C20 H1 FNO sing 105 n n C20 H2 FNO sing 106 n n C20 H3 FNO sing 107 n n C21 H4 FNO sing 108 n n C21 H5 FNO sing 109 n n C21 H6 FNO sing 110 n n C06 H7 FNO sing 111 n n C08 H8 FNO sing 112 n n C08 H9 FNO sing 113 n n C12 H10 FNO sing 114 n n C14 H11 FNO sing 115 n n C18 H12 FNO sing 116 n n C19 H13 FNO sing 117 n n O01 H14 FNO sing 118 n n O03 H15 FNO sing 119 n n O05 H16 FNO sing 120 n n # _atom_sites.entry_id 7CA8 _atom_sites.fract_transf_matrix[1][1] 0.014715 _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] 0.009768 _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] 0.009658 _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 FNO A 1 301 1 FNO LIG . D 3 HOH A 1 401 39 HOH HOH . D 3 HOH A 2 402 22 HOH HOH . D 3 HOH A 3 403 3 HOH HOH . D 3 HOH A 4 404 18 HOH HOH . D 3 HOH A 5 405 34 HOH HOH . D 3 HOH A 6 406 37 HOH HOH . D 3 HOH A 7 407 4 HOH HOH . D 3 HOH A 8 408 10 HOH HOH . D 3 HOH A 9 409 20 HOH HOH . D 3 HOH A 10 410 15 HOH HOH . D 3 HOH A 11 411 17 HOH HOH . D 3 HOH A 12 412 12 HOH HOH . D 3 HOH A 13 413 19 HOH HOH . D 3 HOH A 14 414 9 HOH HOH . D 3 HOH A 15 415 8 HOH HOH . D 3 HOH A 16 416 35 HOH HOH . D 3 HOH A 17 417 7 HOH HOH . D 3 HOH A 18 418 13 HOH HOH . D 3 HOH A 19 419 23 HOH HOH . D 3 HOH A 20 420 38 HOH HOH . D 3 HOH A 21 421 26 HOH HOH . D 3 HOH A 22 422 25 HOH HOH . D 3 HOH A 23 423 29 HOH HOH . D 3 HOH A 24 424 28 HOH HOH . D 3 HOH A 25 425 27 HOH HOH . E 3 HOH B 1 301 24 HOH HOH . E 3 HOH B 2 302 21 HOH HOH . E 3 HOH B 3 303 14 HOH HOH . E 3 HOH B 4 304 5 HOH HOH . E 3 HOH B 5 305 16 HOH HOH . E 3 HOH B 6 306 11 HOH HOH . E 3 HOH B 7 307 30 HOH HOH . E 3 HOH B 8 308 6 HOH HOH . E 3 HOH B 9 309 41 HOH HOH . E 3 HOH B 10 310 36 HOH HOH . E 3 HOH B 11 311 32 HOH HOH . E 3 HOH B 12 312 40 HOH HOH . E 3 HOH B 13 313 1 HOH HOH . E 3 HOH B 14 314 2 HOH HOH . E 3 HOH B 15 315 31 HOH HOH . E 3 HOH B 16 316 33 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 C10 FNO . . . C 2 -22.623 -3.176 -29.331 1 20 ? C10 FNO 301 A 1 HETATM 2 C C13 FNO . . . C 2 -22.505 -0.533 -29.909 1 20 ? C13 FNO 301 A 1 HETATM 3 C C15 FNO . . . C 2 -22.509 -2.652 -26.973 1 20 ? C15 FNO 301 A 1 HETATM 4 C C17 FNO . . . C 2 -20.122 -4.362 -33.728 1 20 ? C17 FNO 301 A 1 HETATM 5 C C20 FNO . . . C 2 -20.149 -2.853 -33.543 1 20 ? C20 FNO 301 A 1 HETATM 6 C C21 FNO . . . C 2 -19.377 -4.937 -34.918 1 20 ? C21 FNO 301 A 1 HETATM 7 C C06 FNO . . . C 2 -22.706 -3.751 -31.799 1 20 ? C06 FNO 301 A 1 HETATM 8 C C07 FNO . . . C 2 -22.647 -2.76 -30.655 1 20 ? C07 FNO 301 A 1 HETATM 9 C C08 FNO . . . C 2 -21.585 -4.749 -31.533 1 20 ? C08 FNO 301 A 1 HETATM 10 C C09 FNO . . . C 2 -22.541 -2.262 -28.298 1 20 ? C09 FNO 301 A 1 HETATM 11 C C11 FNO . . . C 2 -22.482 -0.933 -28.594 1 20 ? C11 FNO 301 A 1 HETATM 12 C C12 FNO . . . C 2 -22.584 -1.423 -30.946 1 20 ? C12 FNO 301 A 1 HETATM 13 C C14 FNO . . . C 2 -20.833 -5.303 -32.751 1 20 ? C14 FNO 301 A 1 HETATM 14 C C16 FNO . . . C 2 -22.4 -0.027 -27.567 1 20 ? C16 FNO 301 A 1 HETATM 15 C C18 FNO . . . C 2 -22.428 -1.753 -25.949 1 20 ? C18 FNO 301 A 1 HETATM 16 C C19 FNO . . . C 2 -22.37 -0.415 -26.254 1 20 ? C19 FNO 301 A 1 HETATM 17 O O01 FNO . . . C 2 -23.934 -4.414 -31.746 1 20 ? O01 FNO 301 A 1 HETATM 18 O O02 FNO . . . C 2 -22.662 -4.358 -29.074 1 20 ? O02 FNO 301 A 1 HETATM 19 O O03 FNO . . . C 2 -22.554 -3.96 -26.719 1 20 ? O03 FNO 301 A 1 HETATM 20 O O04 FNO . . . C 2 -22.455 0.642 -30.183 1 20 ? O04 FNO 301 A 1 HETATM 21 O O05 FNO . . . C 2 -22.352 1.26 -27.9 1 20 ? O05 FNO 301 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #