data_1ZRT # _model_server_result.job_id WWBC0KaNRfRXXSQO35wvvw _model_server_result.datetime_utc '2025-07-07 17:59:43' _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 1zrt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":503}' # _entry.id 1ZRT # _exptl.entry_id 1ZRT _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 113.57 _cell.angle_gamma 90 _cell.entry_id 1ZRT _cell.length_a 95.633 _cell.length_b 154.36 _cell.length_c 103.057 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZRT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _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 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,J,K,L,M,N,O,P,Q,R,S,T,U _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 P 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 B SG CYS 144 D CYS 144 1_555 B SG CYS 167 D CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf2 C SG CYS 138 E CYS 138 1_555 C SG CYS 155 E CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 E SG CYS 144 Q CYS 144 1_555 E SG CYS 167 Q CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf4 F SG CYS 138 R CYS 138 1_555 F SG CYS 155 R CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 B SG CYS 34 D CYS 34 1_555 L CAB HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.796 ? covale ? covale2 B SG CYS 37 D CYS 37 1_555 L CAC HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.804 ? covale ? covale3 E SG CYS 34 Q CYS 34 1_555 S CAB HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.896 ? covale ? covale4 E SG CYS 37 Q CYS 37 1_555 S CAC HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc1 A NE2 HIS 97 C HIS 97 1_555 G FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc2 A NE2 HIS 111 C HIS 111 1_555 H FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc3 A NE2 HIS 198 C HIS 198 1_555 G FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc4 A NE2 HIS 212 C HIS 212 1_555 H FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc5 B NE2 HIS 38 D HIS 38 1_555 L FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc6 B SD MET 183 D MET 183 1_555 L FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc7 C SG CYS 133 E CYS 133 1_555 M FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc8 C ND1 HIS 135 E HIS 135 1_555 M FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc9 C SG CYS 153 E CYS 153 1_555 M FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc10 C N HIS 156 E HIS 156 1_555 M FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc11 C ND1 HIS 156 E HIS 156 1_555 M FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc12 D NE2 HIS 97 P HIS 97 1_555 N FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc13 D NE2 HIS 111 P HIS 111 1_555 O FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc14 D NE2 HIS 198 P HIS 198 1_555 N FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc15 D NE2 HIS 212 P HIS 212 1_555 O FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc16 E NE2 HIS 38 Q HIS 38 1_555 S FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc17 E SD MET 183 Q MET 183 1_555 S FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc18 F SG CYS 133 R CYS 133 1_555 U FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc19 F ND1 HIS 135 R HIS 135 1_555 U FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc20 F SG CYS 153 R CYS 153 1_555 U FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc21 F N HIS 156 R HIS 156 1_555 U FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc22 F ND1 HIS 156 R HIS 156 1_555 U FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? # _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 501 n n O7 C7 SMA sing 502 n n O8 C8 SMA sing 503 n n C7 C8 SMA doub 504 n y C7 C6 SMA sing 505 n y C8 C8A SMA sing 506 n y C6 C5 SMA doub 507 n y C8A O1 SMA sing 508 n n C8A C4A SMA doub 509 n y O1 C2 SMA sing 510 n n C22 C11 SMA sing 511 n n C9 C2 SMA sing 512 n n C9 C10 SMA sing 513 n n C5 C4A SMA sing 514 n y C5 O5 SMA sing 515 n n C4A C4 SMA sing 516 n n C2 C3 SMA doub 517 n n C5M O5 SMA sing 518 n n C3 C4 SMA sing 519 n n C3 C3M SMA sing 520 n n C4 O4 SMA doub 521 n n C11 C10 SMA sing 522 n n C11 C12 SMA sing 523 n n C24 C13 SMA sing 524 n n C12 C13 SMA sing 525 n n C12 O12 SMA sing 526 n n C13 C14 SMA sing 527 n n O12 C23 SMA sing 528 n n O14 C25 SMA sing 529 n n O14 C14 SMA sing 530 n n C14 C15 SMA sing 531 n n C15 C16 SMA doub 532 e n C16 C17 SMA sing 533 n n C17 C18 SMA doub 534 e n C18 C19 SMA sing 535 n n C20 C19 SMA doub 536 e n C20 C21 SMA sing 537 n n C19 C26 SMA sing 538 n n C3M H1 SMA sing 539 n n C3M H2 SMA sing 540 n n C3M H3 SMA sing 541 n n C5M H4 SMA sing 542 n n C5M H5 SMA sing 543 n n C5M H6 SMA sing 544 n n C6 H7 SMA sing 545 n n C7M H8 SMA sing 546 n n C7M H9 SMA sing 547 n n C7M H10 SMA sing 548 n n C9 H11 SMA sing 549 n n C9 H12 SMA sing 550 n n C10 H13 SMA sing 551 n n C10 H14 SMA sing 552 n n C11 H15 SMA sing 553 n n C12 H16 SMA sing 554 n n C13 H17 SMA sing 555 n n C14 H18 SMA sing 556 n n C15 H19 SMA sing 557 n n C16 H21 SMA sing 558 n n C17 H22 SMA sing 559 n n C18 H23 SMA sing 560 n n C20 H25 SMA sing 561 n n C21 H26 SMA sing 562 n n C21 H27 SMA sing 563 n n C21 H28 SMA sing 564 n n C22 H29 SMA sing 565 n n C22 H30 SMA sing 566 n n C22 H31 SMA sing 567 n n C23 H32 SMA sing 568 n n C23 H33 SMA sing 569 n n C23 H34 SMA sing 570 n n C24 H35 SMA sing 571 n n C24 H36 SMA sing 572 n n C24 H37 SMA sing 573 n n C25 H38 SMA sing 574 n n C25 H39 SMA sing 575 n n C25 H40 SMA sing 576 n n C26 H41 SMA sing 577 n n C26 H42 SMA sing 578 n n C26 H43 SMA sing 579 n n O8 H44 SMA sing 580 n n # _atom_sites.entry_id 1ZRT _atom_sites.fract_transf_matrix[1][1] 0.010457 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004562 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006478 _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] 0.010587 _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 C 1 501 501 HEM HEM . H 4 HEM C 1 502 502 HEM HEM . I 5 SMA C 1 503 503 SMA SMA . J 6 UNL C 1 504 504 UNL UNK . K 6 UNL C 1 505 505 UNL UNK . L 7 HEC D 1 501 501 HEC HEC . M 8 FES E 1 501 501 FES FES . N 4 HEM P 1 501 501 HEM HEM . O 4 HEM P 1 502 502 HEM HEM . P 5 SMA P 1 503 503 SMA SMA . Q 6 UNL P 1 504 504 UNL UNK . R 6 UNL P 1 505 505 UNL UNK . S 7 HEC Q 1 501 501 HEC HEC . T 9 PG6 Q 1 502 502 PG6 PG6 . U 8 FES R 1 501 501 FES FES . # 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 . . . I 5 4.615 1.625 0.757 1 91.58 ? C2 SMA 503 C 1 HETATM 2 C C3 SMA . . . I 5 4.542 0.772 -0.446 1 86.51 ? C3 SMA 503 C 1 HETATM 3 C C3M SMA . . . I 5 5.721 0.003 -0.933 1 78.53 ? C3M SMA 503 C 1 HETATM 4 C C4 SMA . . . I 5 3.265 0.682 -1.173 1 94.61 ? C4 SMA 503 C 1 HETATM 5 C C4A SMA . . . I 5 2.08 1.456 -0.614 1 102.41 ? C4A SMA 503 C 1 HETATM 6 C C5 SMA . . . I 5 0.706 1.449 -1.201 1 99.61 ? C5 SMA 503 C 1 HETATM 7 C C5M SMA . . . I 5 0.127 1.468 -3.493 1 109.95 ? C5M SMA 503 C 1 HETATM 8 C C6 SMA . . . I 5 -0.362 2.179 -0.685 1 99.63 ? C6 SMA 503 C 1 HETATM 9 C C7 SMA . . . I 5 -0.243 2.959 0.451 1 104.16 ? C7 SMA 503 C 1 HETATM 10 C C7M SMA . . . I 5 -2.286 4.334 0.263 1 105.95 ? C7M SMA 503 C 1 HETATM 11 C C8 SMA . . . I 5 1.046 3.029 1.149 1 110.01 ? C8 SMA 503 C 1 HETATM 12 C C8A SMA . . . I 5 2.265 2.287 0.622 1 107.27 ? C8A SMA 503 C 1 HETATM 13 C C9 SMA . . . I 5 5.921 1.736 1.465 1 98.66 ? C9 SMA 503 C 1 HETATM 14 C C10 SMA . . . I 5 5.941 0.89 2.731 1 98.51 ? C10 SMA 503 C 1 HETATM 15 C C11 SMA . . . I 5 6.781 1.497 3.877 1 103.06 ? C11 SMA 503 C 1 HETATM 16 C C12 SMA . . . I 5 7.492 0.394 4.693 1 105.08 ? C12 SMA 503 C 1 HETATM 17 C C13 SMA . . . I 5 6.456 -0.438 5.485 1 90.93 ? C13 SMA 503 C 1 HETATM 18 C C14 SMA . . . I 5 7.162 -1.541 6.292 1 98.55 ? C14 SMA 503 C 1 HETATM 19 C C15 SMA . . . I 5 6.375 -2.834 6.361 1 82.33 ? C15 SMA 503 C 1 HETATM 20 C C16 SMA . . . I 5 5.86 -2.952 7.56 1 99.01 ? C16 SMA 503 C 1 HETATM 21 C C17 SMA . . . I 5 5.045 -3.991 8.154 1 110.19 ? C17 SMA 503 C 1 HETATM 22 C C18 SMA . . . I 5 4.535 -3.784 9.38 1 98.38 ? C18 SMA 503 C 1 HETATM 23 C C19 SMA . . . I 5 3.76 -4.918 9.881 1 85.41 ? C19 SMA 503 C 1 HETATM 24 C C20 SMA . . . I 5 2.566 -5.108 9.342 1 91.57 ? C20 SMA 503 C 1 HETATM 25 C C21 SMA . . . I 5 1.667 -6.21 9.742 1 82.64 ? C21 SMA 503 C 1 HETATM 26 C C22 SMA . . . I 5 7.733 2.655 3.489 1 100.17 ? C22 SMA 503 C 1 HETATM 27 C C23 SMA . . . I 5 9.752 -0.346 3.971 1 105.37 ? C23 SMA 503 C 1 HETATM 28 C C24 SMA . . . I 5 5.631 0.484 6.38 1 82.02 ? C24 SMA 503 C 1 HETATM 29 C C25 SMA . . . I 5 8.842 -0.903 7.984 1 96.08 ? C25 SMA 503 C 1 HETATM 30 C C26 SMA . . . I 5 4.343 -5.823 10.923 1 93.97 ? C26 SMA 503 C 1 HETATM 31 O O1 SMA . . . I 5 3.526 2.331 1.227 1 96.08 ? O1 SMA 503 C 1 HETATM 32 O O4 SMA . . . I 5 3.27 -0.035 -2.195 1 86.12 ? O4 SMA 503 C 1 HETATM 33 O O5 SMA . . . I 5 0.491 0.739 -2.328 1 110.86 ? O5 SMA 503 C 1 HETATM 34 O O7 SMA . . . I 5 -1.258 3.695 1.021 1 102.8 ? O7 SMA 503 C 1 HETATM 35 O O8 SMA . . . I 5 1.011 3.847 2.245 1 112.58 ? O8 SMA 503 C 1 HETATM 36 O O12 SMA . . . I 5 8.322 -0.444 3.846 1 106.31 ? O12 SMA 503 C 1 HETATM 37 O O14 SMA . . . I 5 7.462 -1.04 7.614 1 104.69 ? O14 SMA 503 C 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 37 #