data_8WUR # _model_server_result.job_id ITIBLHGGfFf-4br94_qvWg _model_server_result.datetime_utc '2024-11-16 05:23:42' _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 8wur # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 8WUR # _exptl.entry_id 8WUR _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 8WUR _cell.length_a 68.052 _cell.length_b 102.944 _cell.length_c 103.687 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WUR _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 143 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 145 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id C19 _struct_conn.ptnr2_label_comp_id FNO _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id FNO _struct_conn.ptnr2_auth_seq_id 301 _struct_conn.ptnr2_symmetry 1_555 _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 1.574 _struct_conn.pdbx_value_order ? # _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 8WUR _atom_sites.fract_transf_matrix[1][1] 0.014695 _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] 0.009714 _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] 0.009644 _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 77 HOH HOH . D 3 HOH A 2 402 56 HOH HOH . D 3 HOH A 3 403 50 HOH HOH . D 3 HOH A 4 404 34 HOH HOH . D 3 HOH A 5 405 69 HOH HOH . D 3 HOH A 6 406 83 HOH HOH . D 3 HOH A 7 407 26 HOH HOH . D 3 HOH A 8 408 42 HOH HOH . D 3 HOH A 9 409 32 HOH HOH . D 3 HOH A 10 410 63 HOH HOH . D 3 HOH A 11 411 20 HOH HOH . D 3 HOH A 12 412 68 HOH HOH . D 3 HOH A 13 413 78 HOH HOH . D 3 HOH A 14 414 15 HOH HOH . D 3 HOH A 15 415 25 HOH HOH . D 3 HOH A 16 416 59 HOH HOH . D 3 HOH A 17 417 10 HOH HOH . D 3 HOH A 18 418 17 HOH HOH . D 3 HOH A 19 419 21 HOH HOH . D 3 HOH A 20 420 23 HOH HOH . D 3 HOH A 21 421 2 HOH HOH . D 3 HOH A 22 422 31 HOH HOH . D 3 HOH A 23 423 48 HOH HOH . D 3 HOH A 24 424 14 HOH HOH . D 3 HOH A 25 425 89 HOH HOH . D 3 HOH A 26 426 24 HOH HOH . D 3 HOH A 27 427 61 HOH HOH . D 3 HOH A 28 428 5 HOH HOH . D 3 HOH A 29 429 8 HOH HOH . D 3 HOH A 30 430 29 HOH HOH . D 3 HOH A 31 431 41 HOH HOH . D 3 HOH A 32 432 80 HOH HOH . D 3 HOH A 33 433 47 HOH HOH . D 3 HOH A 34 434 71 HOH HOH . D 3 HOH A 35 435 58 HOH HOH . D 3 HOH A 36 436 70 HOH HOH . D 3 HOH A 37 437 54 HOH HOH . D 3 HOH A 38 438 51 HOH HOH . D 3 HOH A 39 439 65 HOH HOH . D 3 HOH A 40 440 43 HOH HOH . D 3 HOH A 41 441 33 HOH HOH . D 3 HOH A 42 442 87 HOH HOH . D 3 HOH A 43 443 9 HOH HOH . D 3 HOH A 44 444 62 HOH HOH . D 3 HOH A 45 445 60 HOH HOH . D 3 HOH A 46 446 52 HOH HOH . D 3 HOH A 47 447 64 HOH HOH . D 3 HOH A 48 448 49 HOH HOH . D 3 HOH A 49 449 73 HOH HOH . D 3 HOH A 50 450 74 HOH HOH . D 3 HOH A 51 451 53 HOH HOH . D 3 HOH A 52 452 85 HOH HOH . D 3 HOH A 53 453 88 HOH HOH . D 3 HOH A 54 454 75 HOH HOH . D 3 HOH A 55 455 18 HOH HOH . E 3 HOH B 1 301 66 HOH HOH . E 3 HOH B 2 302 84 HOH HOH . E 3 HOH B 3 303 1 HOH HOH . E 3 HOH B 4 304 12 HOH HOH . E 3 HOH B 5 305 19 HOH HOH . E 3 HOH B 6 306 55 HOH HOH . E 3 HOH B 7 307 7 HOH HOH . E 3 HOH B 8 308 81 HOH HOH . E 3 HOH B 9 309 28 HOH HOH . E 3 HOH B 10 310 46 HOH HOH . E 3 HOH B 11 311 22 HOH HOH . E 3 HOH B 12 312 45 HOH HOH . E 3 HOH B 13 313 35 HOH HOH . E 3 HOH B 14 314 36 HOH HOH . E 3 HOH B 15 315 16 HOH HOH . E 3 HOH B 16 316 44 HOH HOH . E 3 HOH B 17 317 30 HOH HOH . E 3 HOH B 18 318 6 HOH HOH . E 3 HOH B 19 319 4 HOH HOH . E 3 HOH B 20 320 11 HOH HOH . E 3 HOH B 21 321 3 HOH HOH . E 3 HOH B 22 322 72 HOH HOH . E 3 HOH B 23 323 57 HOH HOH . E 3 HOH B 24 324 90 HOH HOH . E 3 HOH B 25 325 38 HOH HOH . E 3 HOH B 26 326 82 HOH HOH . E 3 HOH B 27 327 27 HOH HOH . E 3 HOH B 28 328 79 HOH HOH . E 3 HOH B 29 329 13 HOH HOH . E 3 HOH B 30 330 76 HOH HOH . E 3 HOH B 31 331 67 HOH HOH . E 3 HOH B 32 332 40 HOH HOH . E 3 HOH B 33 333 37 HOH HOH . E 3 HOH B 34 334 86 HOH HOH . E 3 HOH B 35 335 39 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 -22.734 -3.103 -29.279 1 62.09 ? C10 FNO 301 A 1 HETATM 2 C C13 FNO . . . C 2 -22.567 -0.564 -30.126 1 58.48 ? C13 FNO 301 A 1 HETATM 3 C C15 FNO . . . C 2 -22.549 -2.341 -26.968 1 61.39 ? C15 FNO 301 A 1 HETATM 4 C C17 FNO . . . C 2 -20.217 -4.91 -33.709 1 61.1 ? C17 FNO 301 A 1 HETATM 5 C C20 FNO . . . C 2 -19.213 -4.186 -34.595 1 59.07 ? C20 FNO 301 A 1 HETATM 6 C C21 FNO . . . C 2 -20.788 -6.258 -34.082 1 59.4 ? C21 FNO 301 A 1 HETATM 7 C C06 FNO . . . C 2 -22.915 -4.104 -31.596 1 65.59 ? C06 FNO 301 A 1 HETATM 8 C C07 FNO . . . C 2 -22.776 -2.9 -30.634 1 62.67 ? C07 FNO 301 A 1 HETATM 9 C C08 FNO . . . C 2 -21.634 -4.954 -31.689 1 65.3 ? C08 FNO 301 A 1 HETATM 10 C C09 FNO . . . C 2 -22.586 -2.068 -28.334 1 59.48 ? C09 FNO 301 A 1 HETATM 11 C C11 FNO . . . C 2 -22.527 -0.811 -28.728 1 56.55 ? C11 FNO 301 A 1 HETATM 12 C C12 FNO . . . C 2 -22.676 -1.586 -31.064 1 58.88 ? C12 FNO 301 A 1 HETATM 13 C C14 FNO . . . C 2 -20.612 -4.353 -32.618 1 61.22 ? C14 FNO 301 A 1 HETATM 14 C C16 FNO . . . C 2 -22.408 0.2 -27.734 1 53.45 ? C16 FNO 301 A 1 HETATM 15 C C18 FNO . . . C 2 -22.419 -1.389 -25.999 1 55.89 ? C18 FNO 301 A 1 HETATM 16 C C19 FNO . . . C 2 -22.326 -0.086 -26.392 1 56.34 ? C19 FNO 301 A 1 HETATM 17 O O01 FNO . . . C 2 -23.218 -3.677 -32.85 1 63.57 ? O01 FNO 301 A 1 HETATM 18 O O02 FNO . . . C 2 -22.821 -4.183 -28.914 1 68.42 ? O02 FNO 301 A 1 HETATM 19 O O03 FNO . . . C 2 -22.649 -3.637 -26.58 1 68.84 ? O03 FNO 301 A 1 HETATM 20 O O04 FNO . . . C 2 -22.472 0.531 -30.5 1 57.55 ? O04 FNO 301 A 1 HETATM 21 O O05 FNO . . . C 2 -22.332 1.505 -28.045 1 49.06 ? O05 FNO 301 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #