data_5YBS # _model_server_result.job_id D3Ajtup6z9sZds8QyfQZ_Q _model_server_result.datetime_utc '2025-02-26 21:19:39' _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 5ybs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":303}' # _entry.id 5YBS # _exptl.entry_id 5YBS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 446.576 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'berkeleyone A' _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 5YBS _cell.length_a 171.452 _cell.length_b 171.452 _cell.length_c 45.794 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YBS _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # _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 _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 4 _struct_asym.id G _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 146 A HIS 130 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc2 A OD1 ASP 148 A ASP 132 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc3 A NE2 HIS 230 A HIS 214 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc4 C FE FE . A FE 301 1_555 D O2 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc5 C FE FE . A FE 301 1_555 D O5 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc6 C FE FE . A FE 301 1_555 H O HOH . A HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc7 B NE2 HIS 146 B HIS 130 1_555 E FE FE . B FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc8 B OD1 ASP 148 B ASP 132 1_555 E FE FE . B FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc9 B NE2 HIS 230 B HIS 214 1_555 E FE FE . B FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc10 E FE FE . B FE 301 1_555 F O1 AKG . B AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc11 E FE FE . B FE 301 1_555 F O5 AKG . B AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc12 E FE FE . B FE 301 1_555 I O HOH . B HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? # _chem_comp.formula 'C26 H38 O6' _chem_comp.formula_weight 446.576 _chem_comp.id 8TC _chem_comp.mon_nstd_flag . _chem_comp.name 'berkeleyone A' _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 O01 C02 8TC sing 1 n n C16 C03 8TC sing 2 n n C01 C02 8TC sing 3 n n C01 C06 8TC sing 4 n n C02 C03 8TC sing 5 n n C03 C15 8TC sing 6 n n C03 C04 8TC sing 7 n n C17 C05 8TC sing 8 n n C06 C05 8TC sing 9 n n C05 C04 8TC sing 10 n n C05 C10 8TC sing 11 n n C04 C07 8TC sing 12 n n C07 C08 8TC sing 13 n n C10 C14 8TC sing 14 n n C10 C09 8TC sing 15 n n C14 C13 8TC sing 16 n n C18 C09 8TC sing 17 n n C08 C09 8TC sing 18 n n C09 C11 8TC sing 19 n n C13 C23 8TC sing 20 n n C13 C20 8TC sing 21 n n C13 C12 8TC sing 22 n n O02 C20 8TC doub 23 n n C20 C21 8TC sing 24 n n C11 C12 8TC sing 25 n n C11 C22 8TC sing 26 n n C11 C25 8TC sing 27 n n C12 C19 8TC doub 28 n n C24 C21 8TC sing 29 n n C22 C21 8TC sing 30 n n C22 O03 8TC doub 31 n n C21 O04 8TC sing 32 n n O05 C25 8TC doub 33 n n C25 O06 8TC sing 34 n n O06 C26 8TC sing 35 n n C10 H1 8TC sing 36 n n C15 H2 8TC sing 37 n n C15 H3 8TC sing 38 n n C15 H4 8TC sing 39 n n C17 H5 8TC sing 40 n n C17 H6 8TC sing 41 n n C17 H7 8TC sing 42 n n C24 H8 8TC sing 43 n n C24 H9 8TC sing 44 n n C24 H10 8TC sing 45 n n C26 H11 8TC sing 46 n n C26 H12 8TC sing 47 n n C26 H13 8TC sing 48 n n C01 H14 8TC sing 49 n n C01 H15 8TC sing 50 n n C02 H16 8TC sing 51 n n C04 H17 8TC sing 52 n n C06 H18 8TC sing 53 n n C06 H19 8TC sing 54 n n C07 H20 8TC sing 55 n n C07 H21 8TC sing 56 n n C08 H22 8TC sing 57 n n C08 H23 8TC sing 58 n n C14 H24 8TC sing 59 n n C14 H25 8TC sing 60 n n C16 H26 8TC sing 61 n n C16 H27 8TC sing 62 n n C16 H28 8TC sing 63 n n O01 H29 8TC sing 64 n n C18 H30 8TC sing 65 n n C18 H31 8TC sing 66 n n C18 H32 8TC sing 67 n n C19 H33 8TC sing 68 n n C19 H34 8TC sing 69 n n C23 H35 8TC sing 70 n n C23 H36 8TC sing 71 n n C23 H37 8TC sing 72 n n O04 H38 8TC sing 73 n n # _atom_sites.entry_id 5YBS _atom_sites.fract_transf_matrix[1][1] 0.005833 _atom_sites.fract_transf_matrix[1][2] 0.003367 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006735 _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] 0.021837 _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 FE A 1 301 1 FE FE . D 3 AKG A 1 302 1 AKG AKG . E 2 FE B 1 301 2 FE FE . F 3 AKG B 1 302 2 AKG AKG . G 4 8TC B 1 303 3 8TC LIG . H 5 HOH A 1 401 26 HOH HOH . H 5 HOH A 2 402 18 HOH HOH . H 5 HOH A 3 403 38 HOH HOH . H 5 HOH A 4 404 95 HOH HOH . H 5 HOH A 5 405 52 HOH HOH . H 5 HOH A 6 406 3 HOH HOH . H 5 HOH A 7 407 22 HOH HOH . H 5 HOH A 8 408 133 HOH HOH . H 5 HOH A 9 409 11 HOH HOH . H 5 HOH A 10 410 5 HOH HOH . H 5 HOH A 11 411 74 HOH HOH . H 5 HOH A 12 412 134 HOH HOH . H 5 HOH A 13 413 2 HOH HOH . H 5 HOH A 14 414 8 HOH HOH . H 5 HOH A 15 415 89 HOH HOH . H 5 HOH A 16 416 104 HOH HOH . H 5 HOH A 17 417 6 HOH HOH . H 5 HOH A 18 418 54 HOH HOH . H 5 HOH A 19 419 110 HOH HOH . H 5 HOH A 20 420 76 HOH HOH . H 5 HOH A 21 421 79 HOH HOH . H 5 HOH A 22 422 42 HOH HOH . H 5 HOH A 23 423 94 HOH HOH . H 5 HOH A 24 424 7 HOH HOH . H 5 HOH A 25 425 23 HOH HOH . H 5 HOH A 26 426 34 HOH HOH . H 5 HOH A 27 427 41 HOH HOH . H 5 HOH A 28 428 84 HOH HOH . H 5 HOH A 29 429 62 HOH HOH . H 5 HOH A 30 430 24 HOH HOH . H 5 HOH A 31 431 35 HOH HOH . H 5 HOH A 32 432 43 HOH HOH . H 5 HOH A 33 433 9 HOH HOH . H 5 HOH A 34 434 44 HOH HOH . H 5 HOH A 35 435 51 HOH HOH . H 5 HOH A 36 436 21 HOH HOH . H 5 HOH A 37 437 48 HOH HOH . H 5 HOH A 38 438 17 HOH HOH . H 5 HOH A 39 439 61 HOH HOH . H 5 HOH A 40 440 85 HOH HOH . H 5 HOH A 41 441 32 HOH HOH . H 5 HOH A 42 442 137 HOH HOH . H 5 HOH A 43 443 39 HOH HOH . H 5 HOH A 44 444 31 HOH HOH . H 5 HOH A 45 445 122 HOH HOH . H 5 HOH A 46 446 123 HOH HOH . H 5 HOH A 47 447 93 HOH HOH . H 5 HOH A 48 448 75 HOH HOH . H 5 HOH A 49 449 99 HOH HOH . H 5 HOH A 50 450 97 HOH HOH . H 5 HOH A 51 451 138 HOH HOH . H 5 HOH A 52 452 63 HOH HOH . H 5 HOH A 53 453 124 HOH HOH . H 5 HOH A 54 454 28 HOH HOH . H 5 HOH A 55 455 33 HOH HOH . H 5 HOH A 56 456 148 HOH HOH . H 5 HOH A 57 457 144 HOH HOH . H 5 HOH A 58 458 166 HOH HOH . H 5 HOH A 59 459 146 HOH HOH . H 5 HOH A 60 460 119 HOH HOH . H 5 HOH A 61 461 80 HOH HOH . H 5 HOH A 62 462 46 HOH HOH . H 5 HOH A 63 463 106 HOH HOH . H 5 HOH A 64 464 118 HOH HOH . H 5 HOH A 65 465 170 HOH HOH . H 5 HOH A 66 466 66 HOH HOH . H 5 HOH A 67 467 165 HOH HOH . H 5 HOH A 68 468 158 HOH HOH . H 5 HOH A 69 469 82 HOH HOH . H 5 HOH A 70 470 140 HOH HOH . H 5 HOH A 71 471 157 HOH HOH . H 5 HOH A 72 472 167 HOH HOH . H 5 HOH A 73 473 72 HOH HOH . H 5 HOH A 74 474 181 HOH HOH . I 5 HOH B 1 401 20 HOH HOH . I 5 HOH B 2 402 4 HOH HOH . I 5 HOH B 3 403 57 HOH HOH . I 5 HOH B 4 404 45 HOH HOH . I 5 HOH B 5 405 10 HOH HOH . I 5 HOH B 6 406 69 HOH HOH . I 5 HOH B 7 407 15 HOH HOH . I 5 HOH B 8 408 156 HOH HOH . I 5 HOH B 9 409 27 HOH HOH . I 5 HOH B 10 410 135 HOH HOH . I 5 HOH B 11 411 19 HOH HOH . I 5 HOH B 12 412 30 HOH HOH . I 5 HOH B 13 413 14 HOH HOH . I 5 HOH B 14 414 58 HOH HOH . I 5 HOH B 15 415 16 HOH HOH . I 5 HOH B 16 416 12 HOH HOH . I 5 HOH B 17 417 1 HOH HOH . I 5 HOH B 18 418 64 HOH HOH . I 5 HOH B 19 419 55 HOH HOH . I 5 HOH B 20 420 185 HOH HOH . I 5 HOH B 21 421 111 HOH HOH . I 5 HOH B 22 422 139 HOH HOH . I 5 HOH B 23 423 145 HOH HOH . I 5 HOH B 24 424 154 HOH HOH . I 5 HOH B 25 425 68 HOH HOH . I 5 HOH B 26 426 40 HOH HOH . I 5 HOH B 27 427 92 HOH HOH . I 5 HOH B 28 428 13 HOH HOH . I 5 HOH B 29 429 132 HOH HOH . I 5 HOH B 30 430 77 HOH HOH . I 5 HOH B 31 431 105 HOH HOH . I 5 HOH B 32 432 120 HOH HOH . I 5 HOH B 33 433 73 HOH HOH . I 5 HOH B 34 434 107 HOH HOH . I 5 HOH B 35 435 159 HOH HOH . I 5 HOH B 36 436 142 HOH HOH . I 5 HOH B 37 437 149 HOH HOH . I 5 HOH B 38 438 88 HOH HOH . I 5 HOH B 39 439 184 HOH HOH . I 5 HOH B 40 440 56 HOH HOH . I 5 HOH B 41 441 71 HOH HOH . I 5 HOH B 42 442 60 HOH HOH . I 5 HOH B 43 443 87 HOH HOH . I 5 HOH B 44 444 108 HOH HOH . I 5 HOH B 45 445 173 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 8TC . . . G 4 101.178 216.516 18.311 1 65.96 ? C10 8TC 303 B 1 HETATM 2 C C13 8TC . . . G 4 99.308 215.78 19.942 1 66.83 ? C13 8TC 303 B 1 HETATM 3 C C15 8TC . . . G 4 105.686 216.256 16 1 52.43 ? C15 8TC 303 B 1 HETATM 4 C C17 8TC . . . G 4 101.002 217.273 15.816 1 59.17 ? C17 8TC 303 B 1 HETATM 5 C C20 8TC . . . G 4 100.096 214.539 20.403 1 69.28 ? C20 8TC 303 B 1 HETATM 6 C C21 8TC . . . G 4 101.34 214.736 21.319 1 67.8 ? C21 8TC 303 B 1 HETATM 7 C C22 8TC . . . G 4 101.948 216.18 21.255 1 63.6 ? C22 8TC 303 B 1 HETATM 8 C C24 8TC . . . G 4 102.393 213.674 20.996 1 59.49 ? C24 8TC 303 B 1 HETATM 9 C C26 8TC . . . G 4 100.828 219.337 23.99 1 58.84 ? C26 8TC 303 B 1 HETATM 10 C C01 8TC . . . G 4 102.303 214.647 15.004 1 54.33 ? C01 8TC 303 B 1 HETATM 11 C C02 8TC . . . G 4 103.785 215.024 15.025 1 56.24 ? C02 8TC 303 B 1 HETATM 12 C C03 8TC . . . G 4 104.181 216.389 15.634 1 55.8 ? C03 8TC 303 B 1 HETATM 13 C C04 8TC . . . G 4 103.307 216.645 16.905 1 57.01 ? C04 8TC 303 B 1 HETATM 14 C C05 8TC . . . G 4 101.768 216.379 16.84 1 64.09 ? C05 8TC 303 B 1 HETATM 15 C C06 8TC . . . G 4 101.605 214.908 16.346 1 57.42 ? C06 8TC 303 B 1 HETATM 16 C C07 8TC . . . G 4 103.54 218.004 17.57 1 57.33 ? C07 8TC 303 B 1 HETATM 17 C C08 8TC . . . G 4 102.991 218.113 19.005 1 58.78 ? C08 8TC 303 B 1 HETATM 18 C C09 8TC . . . G 4 101.492 217.779 19.212 1 63.49 ? C09 8TC 303 B 1 HETATM 19 C C11 8TC . . . G 4 101.137 217.423 20.73 1 66.37 ? C11 8TC 303 B 1 HETATM 20 C C12 8TC . . . G 4 99.648 217.037 20.747 1 65.84 ? C12 8TC 303 B 1 HETATM 21 C C14 8TC . . . G 4 99.7 216.062 18.471 1 65.56 ? C14 8TC 303 B 1 HETATM 22 C C16 8TC . . . G 4 104.185 217.536 14.592 1 56.09 ? C16 8TC 303 B 1 HETATM 23 O O01 8TC . . . G 4 104.266 214.942 13.701 1 56.93 ? O01 8TC 303 B 1 HETATM 24 C C18 8TC . . . G 4 100.679 219.043 18.777 1 57.03 ? C18 8TC 303 B 1 HETATM 25 C C19 8TC . . . G 4 98.721 217.655 21.512 1 64.55 ? C19 8TC 303 B 1 HETATM 26 O O02 8TC . . . G 4 99.703 213.44 20.041 1 66.84 ? O02 8TC 303 B 1 HETATM 27 O O03 8TC . . . G 4 103.089 216.344 21.63 1 62.37 ? O03 8TC 303 B 1 HETATM 28 C C23 8TC . . . G 4 97.825 215.344 20.019 1 65.55 ? C23 8TC 303 B 1 HETATM 29 O O04 8TC . . . G 4 100.981 214.398 22.66 1 74.55 ? O04 8TC 303 B 1 HETATM 30 C C25 8TC . . . G 4 101.437 218.505 21.84 1 64.34 ? C25 8TC 303 B 1 HETATM 31 O O05 8TC . . . G 4 101.967 219.553 21.536 1 62.9 ? O05 8TC 303 B 1 HETATM 32 O O06 8TC . . . G 4 101.094 218.245 23.135 1 63.84 ? O06 8TC 303 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #