data_2YIU # _model_server_result.job_id bbXLX--IwUZFwkBkSuJjiw _model_server_result.datetime_utc '2024-11-26 04:04:58' _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 2yiu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":502}' # _entry.id 2YIU # _exptl.entry_id 2YIU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 514.65 _entity.id 5 _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 103.18 _cell.angle_gamma 90 _cell.entry_id 2YIU _cell.length_a 85.3 _cell.length_b 164.91 _cell.length_c 100.61 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YIU _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 PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details software_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 _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 ? 5 I N N ? 5 N 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 C SG CYS 137 C CYS 137 1_555 C SG CYS 154 C CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 F SG CYS 137 F CYS 137 1_555 F SG CYS 154 F CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 B SG CYS 58 B CYS 82 1_555 J CAB HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.63 ? covale ? covale2 B SG CYS 61 B CYS 85 1_555 J CAC HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.673 ? covale ? covale3 E SG CYS 58 E CYS 82 1_555 O CAB HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.627 ? covale ? covale4 E SG CYS 61 E CYS 85 1_555 O CAC HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.664 ? metalc ? metalc1 A NE2 HIS 97 A HIS 97 1_555 G FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc2 A NE2 HIS 111 A HIS 111 1_555 H FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc3 A NE2 HIS 198 A HIS 198 1_555 G FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.829 ? metalc ? metalc4 A NE2 HIS 212 A HIS 212 1_555 H FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc5 B NE2 HIS 62 B HIS 86 1_555 J FE HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc6 B SD MET 186 B MET 210 1_555 J FE HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc7 C SG CYS 132 C CYS 132 1_555 K FE2 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc8 C ND1 HIS 134 C HIS 134 1_555 K FE1 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc9 C SG CYS 152 C CYS 152 1_555 K FE2 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc10 C ND1 HIS 155 C HIS 155 1_555 K FE1 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc11 D NE2 HIS 97 D HIS 97 1_555 L FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc12 D NE2 HIS 111 D HIS 111 1_555 M FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc13 D NE2 HIS 198 D HIS 198 1_555 L FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc14 D NE2 HIS 212 D HIS 212 1_555 M FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc15 E NE2 HIS 62 E HIS 86 1_555 O FE HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc16 E SD MET 186 E MET 210 1_555 O FE HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc17 F SG CYS 132 F CYS 132 1_555 P FE2 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc18 F ND1 HIS 134 F HIS 134 1_555 P FE1 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc19 F SG CYS 152 F CYS 152 1_555 P FE2 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc20 F ND1 HIS 155 F HIS 155 1_555 P FE1 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? # _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 460 n n O7 C7 SMA sing 461 n n O8 C8 SMA sing 462 n n C7 C8 SMA doub 463 n y C7 C6 SMA sing 464 n y C8 C8A SMA sing 465 n y C6 C5 SMA doub 466 n y C8A O1 SMA sing 467 n n C8A C4A SMA doub 468 n y O1 C2 SMA sing 469 n n C22 C11 SMA sing 470 n n C9 C2 SMA sing 471 n n C9 C10 SMA sing 472 n n C5 C4A SMA sing 473 n y C5 O5 SMA sing 474 n n C4A C4 SMA sing 475 n n C2 C3 SMA doub 476 n n C5M O5 SMA sing 477 n n C3 C4 SMA sing 478 n n C3 C3M SMA sing 479 n n C4 O4 SMA doub 480 n n C11 C10 SMA sing 481 n n C11 C12 SMA sing 482 n n C24 C13 SMA sing 483 n n C12 C13 SMA sing 484 n n C12 O12 SMA sing 485 n n C13 C14 SMA sing 486 n n O12 C23 SMA sing 487 n n O14 C25 SMA sing 488 n n O14 C14 SMA sing 489 n n C14 C15 SMA sing 490 n n C15 C16 SMA doub 491 e n C16 C17 SMA sing 492 n n C17 C18 SMA doub 493 e n C18 C19 SMA sing 494 n n C20 C19 SMA doub 495 e n C20 C21 SMA sing 496 n n C19 C26 SMA sing 497 n n C3M H1 SMA sing 498 n n C3M H2 SMA sing 499 n n C3M H3 SMA sing 500 n n C5M H4 SMA sing 501 n n C5M H5 SMA sing 502 n n C5M H6 SMA sing 503 n n C6 H7 SMA sing 504 n n C7M H8 SMA sing 505 n n C7M H9 SMA sing 506 n n C7M H10 SMA sing 507 n n C9 H11 SMA sing 508 n n C9 H12 SMA sing 509 n n C10 H13 SMA sing 510 n n C10 H14 SMA sing 511 n n C11 H15 SMA sing 512 n n C12 H16 SMA sing 513 n n C13 H17 SMA sing 514 n n C14 H18 SMA sing 515 n n C15 H19 SMA sing 516 n n C16 H21 SMA sing 517 n n C17 H22 SMA sing 518 n n C18 H23 SMA sing 519 n n C20 H25 SMA sing 520 n n C21 H26 SMA sing 521 n n C21 H27 SMA sing 522 n n C21 H28 SMA sing 523 n n C22 H29 SMA sing 524 n n C22 H30 SMA sing 525 n n C22 H31 SMA sing 526 n n C23 H32 SMA sing 527 n n C23 H33 SMA sing 528 n n C23 H34 SMA sing 529 n n C24 H35 SMA sing 530 n n C24 H36 SMA sing 531 n n C24 H37 SMA sing 532 n n C25 H38 SMA sing 533 n n C25 H39 SMA sing 534 n n C25 H40 SMA sing 535 n n C26 H41 SMA sing 536 n n C26 H42 SMA sing 537 n n C26 H43 SMA sing 538 n n O8 H44 SMA sing 539 n n # _atom_sites.entry_id 2YIU _atom_sites.fract_transf_matrix[1][1] 0.011723 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002745 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006064 _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] 0.010208 _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 G 4 HEM A 1 500 500 HEM HEM . H 4 HEM A 1 501 501 HEM HEM . I 5 SMA A 1 502 502 SMA SMA . J 6 HEC B 1 500 500 HEC HEC . K 7 FES C 1 500 500 FES FES . L 4 HEM D 1 500 500 HEM HEM . M 4 HEM D 1 501 501 HEM HEM . N 5 SMA D 1 502 502 SMA SMA . O 6 HEC E 1 500 500 HEC HEC . P 7 FES F 1 500 500 FES FES . Q 8 HOH A 1 2001 2001 HOH HOH . Q 8 HOH A 2 2002 2002 HOH HOH . Q 8 HOH A 3 2003 2003 HOH HOH . R 8 HOH B 1 2001 2001 HOH HOH . S 8 HOH D 1 2001 2001 HOH HOH . T 8 HOH F 1 2001 2001 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 C2 SMA . . . N 5 -9.251 -39.645 6.925 1 13.92 ? C2 SMA 502 D 1 HETATM 2 C C3 SMA . . . N 5 -8.843 -39.06 8.123 1 13.47 ? C3 SMA 502 D 1 HETATM 3 C C3M SMA . . . N 5 -8.257 -39.933 9.227 1 11.48 ? C3M SMA 502 D 1 HETATM 4 C C4 SMA . . . N 5 -8.929 -37.678 8.317 1 14.8 ? C4 SMA 502 D 1 HETATM 5 C C4A SMA . . . N 5 -9.535 -36.899 7.346 1 16.38 ? C4A SMA 502 D 1 HETATM 6 C C5 SMA . . . N 5 -9.747 -35.519 7.531 1 15.19 ? C5 SMA 502 D 1 HETATM 7 C C5M SMA . . . N 5 -9.971 -33.604 8.984 1 11.87 ? C5M SMA 502 D 1 HETATM 8 C C6 SMA . . . N 5 -10.369 -34.794 6.514 1 14.2 ? C6 SMA 502 D 1 HETATM 9 C C7 SMA . . . N 5 -10.809 -35.41 5.35 1 12.08 ? C7 SMA 502 D 1 HETATM 10 C C7M SMA . . . N 5 -11.654 -33.306 4.587 1 7.68 ? C7M SMA 502 D 1 HETATM 11 C C8 SMA . . . N 5 -10.604 -36.77 5.174 1 14.76 ? C8 SMA 502 D 1 HETATM 12 C C8A SMA . . . N 5 -9.984 -37.531 6.171 1 16.52 ? C8A SMA 502 D 1 HETATM 13 C C9 SMA . . . N 5 -9.284 -41.168 6.648 1 12.57 ? C9 SMA 502 D 1 HETATM 14 C C10 SMA . . . N 5 -7.981 -41.852 6.224 1 13.2 ? C10 SMA 502 D 1 HETATM 15 C C11 SMA . . . N 5 -8.298 -43.134 5.356 1 13.58 ? C11 SMA 502 D 1 HETATM 16 C C12 SMA . . . N 5 -6.993 -43.806 4.92 1 14.42 ? C12 SMA 502 D 1 HETATM 17 C C13 SMA . . . N 5 -5.96 -43.014 4.12 1 17.92 ? C13 SMA 502 D 1 HETATM 18 C C14 SMA . . . N 5 -4.774 -43.938 3.847 1 21.1 ? C14 SMA 502 D 1 HETATM 19 C C15 SMA . . . N 5 -3.767 -43.119 3.35 1 24.57 ? C15 SMA 502 D 1 HETATM 20 C C16 SMA . . . N 5 -3.423 -43.15 1.998 1 29.04 ? C16 SMA 502 D 1 HETATM 21 C C17 SMA . . . N 5 -2.407 -42.334 1.505 1 31.23 ? C17 SMA 502 D 1 HETATM 22 C C18 SMA . . . N 5 -2.095 -42.363 0.16 1 34.69 ? C18 SMA 502 D 1 HETATM 23 C C19 SMA . . . N 5 -1.122 -41.53 -0.372 1 37.96 ? C19 SMA 502 D 1 HETATM 24 C C20 SMA . . . N 5 -0.827 -41.583 -1.722 1 39.77 ? C20 SMA 502 D 1 HETATM 25 C C21 SMA . . . N 5 0.289 -40.646 -2.198 1 41.35 ? C21 SMA 502 D 1 HETATM 26 C C22 SMA . . . N 5 -9.19 -44.206 6.031 1 6.42 ? C22 SMA 502 D 1 HETATM 27 C C23 SMA . . . N 5 -6.268 -45.561 6.266 1 12.87 ? C23 SMA 502 D 1 HETATM 28 C C24 SMA . . . N 5 -6.545 -42.43 2.836 1 15.71 ? C24 SMA 502 D 1 HETATM 29 C C25 SMA . . . N 5 -4.381 -46.056 2.761 1 18.99 ? C25 SMA 502 D 1 HETATM 30 C C26 SMA . . . N 5 -0.308 -40.554 0.481 1 37.64 ? C26 SMA 502 D 1 HETATM 31 O O1 SMA . . . N 5 -9.827 -38.87 5.949 1 15.07 ? O1 SMA 502 D 1 HETATM 32 O O4 SMA . . . N 5 -8.542 -37.145 9.357 1 13.96 ? O4 SMA 502 D 1 HETATM 33 O O5 SMA . . . N 5 -9.331 -34.878 8.677 1 16.64 ? O5 SMA 502 D 1 HETATM 34 O O7 SMA . . . N 5 -11.441 -34.724 4.369 1 10.69 ? O7 SMA 502 D 1 HETATM 35 O O8 SMA . . . N 5 -11.039 -37.384 4.045 1 13.52 ? O8 SMA 502 D 1 HETATM 36 O O12 SMA . . . N 5 -6.311 -44.125 6.138 1 12.53 ? O12 SMA 502 D 1 HETATM 37 O O14 SMA . . . N 5 -5.311 -44.998 2.976 1 20.59 ? O14 SMA 502 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 37 #