data_1ZYR # _model_server_result.job_id kqWSgkFCHLVvQRSYTEL8OQ _model_server_result.datetime_utc '2024-11-16 06:53:07' _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 1zyr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":1525}' # _entry.id 1ZYR # _exptl.entry_id 1ZYR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 600.7 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description STREPTOLYDIGIN _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 90 _cell.angle_gamma 120 _cell.entry_id 1ZYR _cell.length_a 237 _cell.length_b 237 _cell.length_c 250 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZYR _symmetry.cell_setting trigonal _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,M,N,O,P 1 1 G,H,I,J,K,L,Q,R,S,T 2 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 ? 6 M N N ? 6 Q 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 D SG CYS 1194 D CYS 1194 1_555 D SG CYS 1204 D CYS 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf2 J SG CYS 1112 N CYS 1112 1_555 J SG CYS 1204 N CYS 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? disulf ? disulf3 J SG CYS 1201 N CYS 1201 1_555 J SG CYS 1204 N CYS 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 D SG CYS 58 D CYS 58 1_555 N ZN ZN . D ZN 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc2 D SG CYS 60 D CYS 60 1_555 N ZN ZN . D ZN 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc3 D SG CYS 76 D CYS 76 1_555 N ZN ZN . D ZN 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc4 D OD1 ASP 739 D ASP 739 1_555 P MG MG . D MG 9901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc5 D OD2 ASP 741 D ASP 741 1_555 P MG MG . D MG 9901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc6 D OG1 THR 1196 D THR 1196 1_555 O ZN ZN . D ZN 9002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc7 J SG CYS 60 N CYS 60 1_555 R ZN ZN . N ZN 9003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc8 J SG CYS 73 N CYS 73 1_555 R ZN ZN . N ZN 9003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.754 ? metalc ? metalc9 J OD1 ASP 739 N ASP 739 1_555 T MG MG . N MG 9902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc10 J OD1 ASP 741 N ASP 741 1_555 T MG MG . N MG 9902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc11 J OD1 ASP 743 N ASP 743 1_555 T MG MG . N MG 9902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc12 J OD2 ASP 743 N ASP 743 1_555 T MG MG . N MG 9902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? metalc ? metalc13 J SG CYS 1112 N CYS 1112 1_555 S ZN ZN . N ZN 9004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc14 J SG CYS 1204 N CYS 1204 1_555 S ZN ZN . N ZN 9004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? # _chem_comp.formula 'C32 H44 N2 O9' _chem_comp.formula_weight 600.7 _chem_comp.id STD _chem_comp.mon_nstd_flag . _chem_comp.name STREPTOLYDIGIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 2-PYRROLIDINEACETAMIDE;PORTAMYCIN # 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 C1 C2 STD sing 288 n n C1 C3 STD sing 289 n n C1 C5 STD doub 290 e n C2 N1 STD sing 291 n n C2 O2 STD doub 292 n n N1 C4 STD sing 293 n n N1 C20 STD sing 294 n n C3 O1 STD doub 295 n n C3 C20 STD sing 296 n n C4 O4 STD sing 297 n n C4 C12 STD sing 298 n n C4 H4 STD sing 299 n n C5 C6 STD sing 300 n n C5 O3 STD sing 301 n n C6 C7 STD doub 302 e n C6 H6 STD sing 303 n n C7 C8 STD sing 304 n n C7 H7 STD sing 305 n n C8 C9 STD doub 306 e n C8 C11 STD sing 307 n n C9 C10 STD sing 308 n n C9 H9 STD sing 309 n n C10 C13 STD sing 310 n n C10 C14 STD sing 311 n n C10 H10 STD sing 312 n n C11 H111 STD sing 313 n n C11 H112 STD sing 314 n n C11 H113 STD sing 315 n n O3 HO3 STD sing 316 n n O4 C25 STD sing 317 n n C12 C15 STD sing 318 n n C12 H121 STD sing 319 n n C12 H122 STD sing 320 n n C13 C16 STD sing 321 n n C13 O5 STD sing 322 n n C13 H13 STD sing 323 n n C14 H141 STD sing 324 n n C14 H142 STD sing 325 n n C14 H143 STD sing 326 n n C15 C26 STD sing 327 n n C15 H151 STD sing 328 n n C15 H152 STD sing 329 n n C16 C17 STD sing 330 n n C16 C18 STD sing 331 n n C16 H16 STD sing 332 n n O5 C19 STD sing 333 n n C17 O8 STD sing 334 n n C17 C30 STD sing 335 n n C17 H17 STD sing 336 n n C18 H181 STD sing 337 n n C18 H182 STD sing 338 n n C18 H183 STD sing 339 n n C19 O8 STD sing 340 n n C19 C28 STD sing 341 n n C19 C29 STD sing 342 n n C20 C21 STD sing 343 n n C20 H20 STD sing 344 n n C21 C22 STD sing 345 n n C21 C23 STD sing 346 n n C21 H21 STD sing 347 n n C22 N2 STD sing 348 n n C22 O6 STD doub 349 n n C23 H231 STD sing 350 n n C23 H232 STD sing 351 n n C23 H233 STD sing 352 n n N2 C24 STD sing 353 n n N2 HN2 STD sing 354 n n C24 H241 STD sing 355 n n C24 H242 STD sing 356 n n C24 H243 STD sing 357 n n C25 C26 STD sing 358 n n C25 C27 STD sing 359 n n C25 H25 STD sing 360 n n C26 O7 STD sing 361 n n C26 H26 STD sing 362 n n O7 HO7 STD sing 363 n n C27 H271 STD sing 364 n n C27 H272 STD sing 365 n n C27 H273 STD sing 366 n n C28 C31 STD sing 367 n n C28 C32 STD sing 368 n n C28 O9 STD sing 369 n n C29 H291 STD sing 370 n n C29 H292 STD sing 371 n n C29 H293 STD sing 372 n n C30 C32 STD doub 373 n n C30 H30 STD sing 374 n n C31 O9 STD sing 375 n n C31 H311 STD sing 376 n n C31 H312 STD sing 377 n n C32 H32 STD sing 378 n n # _atom_sites.entry_id 1ZYR _atom_sites.fract_transf_matrix[1][1] 0.004219 _atom_sites.fract_transf_matrix[1][2] 0.002436 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004872 _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] 0.004 _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 M 6 STD D 1 1525 1 STD STD . N 7 ZN D 1 9001 9001 ZN ZN . O 7 ZN D 1 9002 9002 ZN ZN . P 8 MG D 1 9901 9901 MG MG . Q 6 STD M 1 1120 2 STD STD . R 7 ZN N 1 9003 9003 ZN ZN . S 7 ZN N 1 9004 9004 ZN ZN . T 8 MG N 1 9902 9902 MG MG . # 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 C1 STD . . . M 6 -27.594 -44.534 -22.329 1 60.14 ? C1 STD 1525 D 1 HETATM 2 C C2 STD . . . M 6 -26.914 -43.292 -22.551 1 60.18 ? C2 STD 1525 D 1 HETATM 3 N N1 STD . . . M 6 -26.177 -43.394 -23.759 1 59.77 ? N1 STD 1525 D 1 HETATM 4 C C3 STD . . . M 6 -27.159 -45.371 -23.435 1 60.51 ? C3 STD 1525 D 1 HETATM 5 C C4 STD . . . M 6 -25.85 -42.234 -24.514 1 60.42 ? C4 STD 1525 D 1 HETATM 6 O O1 STD . . . M 6 -27.745 -46.431 -23.795 1 60.66 ? O1 STD 1525 D 1 HETATM 7 O O2 STD . . . M 6 -26.995 -42.247 -21.9 1 60.03 ? O2 STD 1525 D 1 HETATM 8 C C5 STD . . . M 6 -28.516 -44.835 -21.361 1 59.3 ? C5 STD 1525 D 1 HETATM 9 C C6 STD . . . M 6 -28.944 -43.924 -20.342 1 56.44 ? C6 STD 1525 D 1 HETATM 10 C C7 STD . . . M 6 -29.84 -44.235 -19.424 1 54.02 ? C7 STD 1525 D 1 HETATM 11 C C8 STD . . . M 6 -30.225 -43.37 -18.364 1 51.85 ? C8 STD 1525 D 1 HETATM 12 C C9 STD . . . M 6 -31.062 -43.874 -17.489 1 48.02 ? C9 STD 1525 D 1 HETATM 13 C C10 STD . . . M 6 -31.491 -43.209 -16.253 1 46.23 ? C10 STD 1525 D 1 HETATM 14 C C11 STD . . . M 6 -29.621 -41.963 -18.281 1 52.35 ? C11 STD 1525 D 1 HETATM 15 O O3 STD . . . M 6 -29.089 -46.096 -21.331 1 61.33 ? O3 STD 1525 D 1 HETATM 16 O O4 STD . . . M 6 -27.085 -41.495 -24.682 1 61.17 ? O4 STD 1525 D 1 HETATM 17 C C12 STD . . . M 6 -24.709 -41.438 -23.791 1 59.65 ? C12 STD 1525 D 1 HETATM 18 C C13 STD . . . M 6 -30.344 -43.217 -15.172 1 43.79 ? C13 STD 1525 D 1 HETATM 19 C C14 STD . . . M 6 -32.791 -43.904 -15.765 1 45.78 ? C14 STD 1525 D 1 HETATM 20 C C15 STD . . . M 6 -24.497 -40.13 -24.556 1 62.72 ? C15 STD 1525 D 1 HETATM 21 C C16 STD . . . M 6 -29.993 -44.627 -14.479 1 43.14 ? C16 STD 1525 D 1 HETATM 22 O O5 STD . . . M 6 -30.821 -42.323 -14.147 1 45.08 ? O5 STD 1525 D 1 HETATM 23 C C17 STD . . . M 6 -29.066 -44.382 -13.231 1 44.73 ? C17 STD 1525 D 1 HETATM 24 C C18 STD . . . M 6 -29.287 -45.645 -15.422 1 39.39 ? C18 STD 1525 D 1 HETATM 25 C C19 STD . . . M 6 -30.003 -42.171 -12.94 1 47.04 ? C19 STD 1525 D 1 HETATM 26 C C20 STD . . . M 6 -25.912 -44.81 -24.117 1 60.02 ? C20 STD 1525 D 1 HETATM 27 C C21 STD . . . M 6 -24.539 -45.03 -23.401 1 59.36 ? C21 STD 1525 D 1 HETATM 28 C C22 STD . . . M 6 -24.353 -46.2 -22.474 1 59.44 ? C22 STD 1525 D 1 HETATM 29 C C23 STD . . . M 6 -23.336 -44.951 -24.392 1 59.18 ? C23 STD 1525 D 1 HETATM 30 N N2 STD . . . M 6 -24.172 -45.804 -21.147 1 59.79 ? N2 STD 1525 D 1 HETATM 31 O O6 STD . . . M 6 -24.358 -47.396 -22.808 1 59.54 ? O6 STD 1525 D 1 HETATM 32 C C24 STD . . . M 6 -23.943 -46.762 -20.06 1 60.08 ? C24 STD 1525 D 1 HETATM 33 C C25 STD . . . M 6 -26.927 -40.24 -25.389 1 63.46 ? C25 STD 1525 D 1 HETATM 34 C C26 STD . . . M 6 -25.852 -39.341 -24.61 1 63.73 ? C26 STD 1525 D 1 HETATM 35 O O7 STD . . . M 6 -26.289 -39.094 -23.239 1 62.17 ? O7 STD 1525 D 1 HETATM 36 C C27 STD . . . M 6 -28.318 -39.545 -25.539 1 61.02 ? C27 STD 1525 D 1 HETATM 37 O O8 STD . . . M 6 -29.784 -43.481 -12.326 1 45.79 ? O8 STD 1525 D 1 HETATM 38 C C28 STD . . . M 6 -28.611 -41.456 -13.2 1 48.74 ? C28 STD 1525 D 1 HETATM 39 C C29 STD . . . M 6 -30.831 -41.304 -11.979 1 48.09 ? C29 STD 1525 D 1 HETATM 40 C C30 STD . . . M 6 -27.697 -43.775 -13.572 1 46.81 ? C30 STD 1525 D 1 HETATM 41 C C31 STD . . . M 6 -28.768 -40.205 -14.015 1 50.35 ? C31 STD 1525 D 1 HETATM 42 C C32 STD . . . M 6 -27.49 -42.445 -13.543 1 47.87 ? C32 STD 1525 D 1 HETATM 43 O O9 STD . . . M 6 -28.162 -40.237 -12.729 1 49.93 ? O9 STD 1525 D 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 191 _model_server_stats.query_time_ms 556 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #