data_1KYO # _model_server_result.job_id 9DiUND7J3DZQQ_dim471qQ _model_server_result.datetime_utc '2024-12-21 14:52:37' _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 1kyo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":505}' # _entry.id 1KYO # _exptl.entry_id 1KYO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 514.65 _entity.id 14 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'STIGMATELLIN A' _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 104.19 _cell.angle_gamma 90 _cell.entry_id 1KYO _cell.length_a 147.224 _cell.length_b 165.531 _cell.length_c 195.889 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KYO _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 23-meric _pdbx_struct_assembly.oligomeric_count 23 _pdbx_struct_assembly.details author_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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA _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 ? 14 Z N N ? 14 EA 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 disulf ? disulf1 E SG CYS 134 E CYS 164 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 F SG CYS 28 F CYS 101 1_555 F SG CYS 50 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 J SG CYS 22 J CYS 22 1_555 J SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 K SG CYS 23 K CYS 23 1_555 K SG CYS 88 K CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 P SG CYS 134 P CYS 164 1_555 P SG CYS 150 P CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 Q SG CYS 28 Q CYS 101 1_555 Q SG CYS 50 Q CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf7 U SG CYS 22 U CYS 22 1_555 U SG CYS 96 U CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 V SG CYS 23 V CYS 23 1_555 V SG CYS 88 V CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 D SG CYS 40 D CYS 101 1_555 AA CAB HEC . D HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.806 ? covale ? covale2 D SG CYS 43 D CYS 104 1_555 AA CAC HEC . D HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale3 O SG CYS 40 O CYS 101 1_555 FA CAB HEC . O HEC 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? covale ? covale4 O SG CYS 43 O CYS 104 1_555 FA CAC HEC . O HEC 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.832 ? covale ? covale5 W SG CYS 19 W CYS 19 1_555 HA CAB HEC . W HEC 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.803 ? covale ? covale6 W SG CYS 22 W CYS 22 1_555 HA CAC HEC . W HEC 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.817 ? covale ? covale7 W C PRO 76 W PRO 76 1_555 W N M3L 77 W M3L 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale8 W C M3L 77 W M3L 77 1_555 W N LYS 78 W LYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 C NE2 HIS 82 C HIS 82 1_555 X FE HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc2 C NE2 HIS 96 C HIS 96 1_555 Y FE HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc3 C NE2 HIS 183 C HIS 183 1_555 X FE HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc4 C NE2 HIS 197 C HIS 197 1_555 Y FE HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 AA FE HEC . D HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc6 D SD MET 164 D MET 225 1_555 AA FE HEC . D HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc7 E SG CYS 129 E CYS 159 1_555 BA FE1 FES . E FES 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc8 E ND1 HIS 131 E HIS 161 1_555 BA FE2 FES . E FES 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc9 E SG CYS 148 E CYS 178 1_555 BA FE1 FES . E FES 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc10 E ND1 HIS 151 E HIS 181 1_555 BA FE2 FES . E FES 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc11 N NE2 HIS 82 N HIS 82 1_555 CA FE HEC . N HEC 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc12 N NE2 HIS 96 N HIS 96 1_555 DA FE HEC . N HEC 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc13 N NE2 HIS 183 N HIS 183 1_555 CA FE HEC . N HEC 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc14 N NE2 HIS 197 N HIS 197 1_555 DA FE HEC . N HEC 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc15 O NE2 HIS 44 O HIS 105 1_555 FA FE HEC . O HEC 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc16 O SD MET 164 O MET 225 1_555 FA FE HEC . O HEC 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc17 P SG CYS 129 P CYS 159 1_555 GA FE1 FES . P FES 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc18 P ND1 HIS 131 P HIS 161 1_555 GA FE2 FES . P FES 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc19 P SG CYS 148 P CYS 178 1_555 GA FE1 FES . P FES 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc20 P ND1 HIS 151 P HIS 181 1_555 GA FE2 FES . P FES 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc21 W NE2 HIS 23 W HIS 23 1_555 HA FE HEC . W HEC 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc22 W SD MET 85 W MET 85 1_555 HA FE HEC . W HEC 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? # _chem_comp.formula 'C30 H42 O7' _chem_comp.formula_weight 514.65 _chem_comp.id SMA _chem_comp.mon_nstd_flag . _chem_comp.name 'STIGMATELLIN 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 C7M O7 SMA sing 409 n n O7 C7 SMA sing 410 n n O8 C8 SMA sing 411 n n C7 C8 SMA doub 412 n y C7 C6 SMA sing 413 n y C8 C8A SMA sing 414 n y C6 C5 SMA doub 415 n y C8A O1 SMA sing 416 n n C8A C4A SMA doub 417 n y O1 C2 SMA sing 418 n n C22 C11 SMA sing 419 n n C9 C2 SMA sing 420 n n C9 C10 SMA sing 421 n n C5 C4A SMA sing 422 n y C5 O5 SMA sing 423 n n C4A C4 SMA sing 424 n n C2 C3 SMA doub 425 n n C5M O5 SMA sing 426 n n C3 C4 SMA sing 427 n n C3 C3M SMA sing 428 n n C4 O4 SMA doub 429 n n C11 C10 SMA sing 430 n n C11 C12 SMA sing 431 n n C24 C13 SMA sing 432 n n C12 C13 SMA sing 433 n n C12 O12 SMA sing 434 n n C13 C14 SMA sing 435 n n O12 C23 SMA sing 436 n n O14 C25 SMA sing 437 n n O14 C14 SMA sing 438 n n C14 C15 SMA sing 439 n n C15 C16 SMA doub 440 e n C16 C17 SMA sing 441 n n C17 C18 SMA doub 442 e n C18 C19 SMA sing 443 n n C20 C19 SMA doub 444 e n C20 C21 SMA sing 445 n n C19 C26 SMA sing 446 n n C3M H1 SMA sing 447 n n C3M H2 SMA sing 448 n n C3M H3 SMA sing 449 n n C5M H4 SMA sing 450 n n C5M H5 SMA sing 451 n n C5M H6 SMA sing 452 n n C6 H7 SMA sing 453 n n C7M H8 SMA sing 454 n n C7M H9 SMA sing 455 n n C7M H10 SMA sing 456 n n C9 H11 SMA sing 457 n n C9 H12 SMA sing 458 n n C10 H13 SMA sing 459 n n C10 H14 SMA sing 460 n n C11 H15 SMA sing 461 n n C12 H16 SMA sing 462 n n C13 H17 SMA sing 463 n n C14 H18 SMA sing 464 n n C15 H19 SMA sing 465 n n C16 H21 SMA sing 466 n n C17 H22 SMA sing 467 n n C18 H23 SMA sing 468 n n C20 H25 SMA sing 469 n n C21 H26 SMA sing 470 n n C21 H27 SMA sing 471 n n C21 H28 SMA sing 472 n n C22 H29 SMA sing 473 n n C22 H30 SMA sing 474 n n C22 H31 SMA sing 475 n n C23 H32 SMA sing 476 n n C23 H33 SMA sing 477 n n C23 H34 SMA sing 478 n n C24 H35 SMA sing 479 n n C24 H36 SMA sing 480 n n C24 H37 SMA sing 481 n n C25 H38 SMA sing 482 n n C25 H39 SMA sing 483 n n C25 H40 SMA sing 484 n n C26 H41 SMA sing 485 n n C26 H42 SMA sing 486 n n C26 H43 SMA sing 487 n n O8 H44 SMA sing 488 n n # _atom_sites.entry_id 1KYO _atom_sites.fract_transf_matrix[1][1] 0.006792 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001718 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006041 _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] 0.005266 _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 X 13 HEC C 1 501 1 HEC HEM . Y 13 HEC C 1 502 2 HEC HEM . Z 14 SMA C 1 505 5 SMA STG . AA 13 HEC D 1 503 3 HEC HEM . BA 15 FES E 1 504 4 FES FES . CA 13 HEC N 1 521 21 HEC HEM . DA 13 HEC N 1 522 22 HEC HEM . EA 14 SMA N 1 525 25 SMA STG . FA 13 HEC O 1 523 23 HEC HEM . GA 15 FES P 1 524 24 FES FES . HA 13 HEC W 1 526 26 HEC HEM . # 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 C2 SMA . . . Z 14 17.323 -22.376 71.582 1 14.44 ? C2 SMA 505 C 1 HETATM 2 C C3 SMA . . . Z 14 16.419 -22.963 72.371 1 13.41 ? C3 SMA 505 C 1 HETATM 3 C C3M SMA . . . Z 14 15.271 -22.16 72.94 1 15.06 ? C3M SMA 505 C 1 HETATM 4 C C4 SMA . . . Z 14 16.491 -24.363 72.716 1 15.01 ? C4 SMA 505 C 1 HETATM 5 C C4A SMA . . . Z 14 17.628 -25.117 72.158 1 14.23 ? C4A SMA 505 C 1 HETATM 6 C C5 SMA . . . Z 14 17.833 -26.536 72.424 1 14.93 ? C5 SMA 505 C 1 HETATM 7 C C5M SMA . . . Z 14 17.464 -27.859 74.321 1 19.54 ? C5M SMA 505 C 1 HETATM 8 C C6 SMA . . . Z 14 18.911 -27.19 71.884 1 15.1 ? C6 SMA 505 C 1 HETATM 9 C C7 SMA . . . Z 14 19.825 -26.496 71.052 1 16.12 ? C7 SMA 505 C 1 HETATM 10 C C7M SMA . . . Z 14 21.355 -28.293 71.205 1 18.54 ? C7M SMA 505 C 1 HETATM 11 C C8 SMA . . . Z 14 19.683 -25.133 70.754 1 13.19 ? C8 SMA 505 C 1 HETATM 12 C C8A SMA . . . Z 14 18.594 -24.424 71.288 1 12.76 ? C8A SMA 505 C 1 HETATM 13 C C9 SMA . . . Z 14 17.207 -20.904 71.253 1 15.42 ? C9 SMA 505 C 1 HETATM 14 C C10 SMA . . . Z 14 17.579 -20.577 69.848 1 18.86 ? C10 SMA 505 C 1 HETATM 15 C C11 SMA . . . Z 14 17.499 -19.11 69.431 1 17.78 ? C11 SMA 505 C 1 HETATM 16 C C12 SMA . . . Z 14 16.209 -18.915 68.581 1 19.42 ? C12 SMA 505 C 1 HETATM 17 C C13 SMA . . . Z 14 16.462 -19.546 67.11 1 18.41 ? C13 SMA 505 C 1 HETATM 18 C C14 SMA . . . Z 14 15.772 -18.766 65.954 1 19.13 ? C14 SMA 505 C 1 HETATM 19 C C15 SMA . . . Z 14 15.116 -19.691 64.954 1 18.99 ? C15 SMA 505 C 1 HETATM 20 C C16 SMA . . . Z 14 15.075 -19.48 63.619 1 19.44 ? C16 SMA 505 C 1 HETATM 21 C C17 SMA . . . Z 14 15.193 -20.508 62.574 1 20.07 ? C17 SMA 505 C 1 HETATM 22 C C18 SMA . . . Z 14 14.142 -21.041 61.906 1 17.72 ? C18 SMA 505 C 1 HETATM 23 C C19 SMA . . . Z 14 14.169 -21.554 60.54 1 16.34 ? C19 SMA 505 C 1 HETATM 24 C C20 SMA . . . Z 14 14.869 -21.021 59.497 1 14.55 ? C20 SMA 505 C 1 HETATM 25 C C21 SMA . . . Z 14 14.875 -21.575 58.079 1 12.96 ? C21 SMA 505 C 1 HETATM 26 C C22 SMA . . . Z 14 17.531 -18.193 70.64 1 19.77 ? C22 SMA 505 C 1 HETATM 27 C C23 SMA . . . Z 14 14.558 -17.428 69.116 1 17.8 ? C23 SMA 505 C 1 HETATM 28 C C24 SMA . . . Z 14 17.931 -19.641 66.773 1 17.88 ? C24 SMA 505 C 1 HETATM 29 C C25 SMA . . . Z 14 16.761 -16.892 65.038 1 18.35 ? C25 SMA 505 C 1 HETATM 30 C C26 SMA . . . Z 14 13.279 -22.781 60.482 1 16.09 ? C26 SMA 505 C 1 HETATM 31 O O1 SMA . . . Z 14 18.403 -23.075 71.036 1 15.25 ? O1 SMA 505 C 1 HETATM 32 O O4 SMA . . . Z 14 15.651 -24.908 73.446 1 18.89 ? O4 SMA 505 C 1 HETATM 33 O O5 SMA . . . Z 14 16.922 -27.196 73.236 1 17.8 ? O5 SMA 505 C 1 HETATM 34 O O7 SMA . . . Z 14 20.921 -27.176 70.502 1 18.56 ? O7 SMA 505 C 1 HETATM 35 O O8 SMA . . . Z 14 20.588 -24.54 69.955 1 14.37 ? O8 SMA 505 C 1 HETATM 36 O O12 SMA . . . Z 14 15.813 -17.583 68.562 1 21.24 ? O12 SMA 505 C 1 HETATM 37 O O14 SMA . . . Z 14 15.832 -17.378 65.935 1 20.14 ? O14 SMA 505 C 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 37 #