data_7KNJ # _model_server_result.job_id I9VcGoHn8espG3z2XgTcAw _model_server_result.datetime_utc '2024-11-05 21:09:16' _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 7knj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":305}' # _entry.id 7KNJ # _exptl.entry_id 7KNJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 504.612 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Phorbol 12,13-dibutyrate' _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 96.92 _cell.angle_gamma 90 _cell.entry_id 7KNJ _cell.length_a 34.205 _cell.length_b 26.138 _cell.length_c 58.158 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KNJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 F _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 ND1 HIS 3 A HIS 231 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc2 A SG CYS 16 A CYS 244 1_555 E ZN ZN . A ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc3 A SG CYS 19 A CYS 247 1_555 E ZN ZN . A ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc4 A SG CYS 33 A CYS 261 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc5 A SG CYS 36 A CYS 264 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc6 A ND1 HIS 41 A HIS 269 1_555 E ZN ZN . A ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc7 A SG CYS 44 A CYS 272 1_555 E ZN ZN . A ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc8 A SG CYS 52 A CYS 280 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? # _chem_comp.formula 'C28 H40 O8' _chem_comp.formula_weight 504.612 _chem_comp.id WTS _chem_comp.mon_nstd_flag . _chem_comp.name 'Phorbol 12,13-dibutyrate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(1aR,1bS,4aR,7aS,7bS,8R,9R,9aS)-4a,7b-dihydroxy-3-(hydroxymethyl)-1,1,6,8-tetramethyl-5-oxo-1,1a,1b,4,4a,5,7a,7b,8,9-decahydro-9aH-cyclopropa[3,4]benzo[1,2-e]azulene-9,9a-diyl dibutanoate' # 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 C26 C25 WTS sing 355 n n C26 C27 WTS sing 356 n n O8 C25 WTS doub 357 n n C25 O7 WTS sing 358 n n C27 C28 WTS sing 359 n n C23 C24 WTS sing 360 n n C23 C22 WTS sing 361 n n C1 C2 WTS sing 362 n n O7 C3 WTS sing 363 n n C22 C21 WTS sing 364 n n C3 C2 WTS sing 365 n n C3 C4 WTS sing 366 n n C21 O6 WTS doub 367 n n C21 O5 WTS sing 368 n n O5 C4 WTS sing 369 n n C2 C7 WTS sing 370 n n C16 C14 WTS sing 371 n n C4 C18 WTS sing 372 n n C4 C5 WTS sing 373 n n O1 C7 WTS sing 374 n n C15 C14 WTS doub 375 n n C15 C8 WTS sing 376 n n C14 C13 WTS sing 377 n n C7 C8 WTS sing 378 n n C7 C6 WTS sing 379 n n C18 C19 WTS sing 380 n n C18 C5 WTS sing 381 n n C18 C20 WTS sing 382 n n C8 C9 WTS sing 383 n n C5 C6 WTS sing 384 n n C13 C9 WTS sing 385 n n C13 O3 WTS doub 386 n n C6 C12 WTS sing 387 n n O2 C9 WTS sing 388 n n C9 C10 WTS sing 389 n n C12 C11 WTS doub 390 n n C10 C11 WTS sing 391 n n C11 C17 WTS sing 392 n n C17 O4 WTS sing 393 n n C16 H1 WTS sing 394 n n C16 H2 WTS sing 395 n n C16 H3 WTS sing 396 n n C15 H4 WTS sing 397 n n C10 H7 WTS sing 398 n n C10 H8 WTS sing 399 n n C12 H9 WTS sing 400 n n C8 H10 WTS sing 401 n n O1 H11 WTS sing 402 n n C2 H12 WTS sing 403 n n C6 H13 WTS sing 404 n n C5 H14 WTS sing 405 n n C3 H15 WTS sing 406 n n C1 H16 WTS sing 407 n n C1 H17 WTS sing 408 n n C1 H18 WTS sing 409 n n C17 H19 WTS sing 410 n n C17 H20 WTS sing 411 n n C19 H21 WTS sing 412 n n C19 H22 WTS sing 413 n n C19 H23 WTS sing 414 n n C20 H24 WTS sing 415 n n C20 H25 WTS sing 416 n n C20 H26 WTS sing 417 n n C22 H27 WTS sing 418 n n C22 H28 WTS sing 419 n n C23 H29 WTS sing 420 n n C23 H30 WTS sing 421 n n C24 H31 WTS sing 422 n n C24 H32 WTS sing 423 n n C24 H33 WTS sing 424 n n C26 H34 WTS sing 425 n n C26 H35 WTS sing 426 n n C27 H36 WTS sing 427 n n C27 H37 WTS sing 428 n n C28 H38 WTS sing 429 n n C28 H39 WTS sing 430 n n C28 H40 WTS sing 431 n n O2 H41 WTS sing 432 n n O4 H42 WTS sing 433 n n # _atom_sites.entry_id 7KNJ _atom_sites.fract_transf_matrix[1][1] 0.029235 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003546 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.038258 _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] 0.017321 _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 B 2 XP5 A 1 301 2 XP5 PCL . C 2 XP5 A 1 302 3 XP5 PCL . D 3 ZN A 1 303 1 ZN ZN . E 3 ZN A 1 304 2 ZN ZN . F 4 WTS A 1 305 1 WTS 99G . G 5 HOH A 1 401 26 HOH HOH . G 5 HOH A 2 402 23 HOH HOH . G 5 HOH A 3 403 21 HOH HOH . G 5 HOH A 4 404 34 HOH HOH . G 5 HOH A 5 405 30 HOH HOH . G 5 HOH A 6 406 45 HOH HOH . G 5 HOH A 7 407 15 HOH HOH . G 5 HOH A 8 408 28 HOH HOH . G 5 HOH A 9 409 16 HOH HOH . G 5 HOH A 10 410 32 HOH HOH . G 5 HOH A 11 411 14 HOH HOH . G 5 HOH A 12 412 7 HOH HOH . G 5 HOH A 13 413 13 HOH HOH . G 5 HOH A 14 414 4 HOH HOH . G 5 HOH A 15 415 27 HOH HOH . G 5 HOH A 16 416 19 HOH HOH . G 5 HOH A 17 417 41 HOH HOH . G 5 HOH A 18 418 8 HOH HOH . G 5 HOH A 19 419 10 HOH HOH . G 5 HOH A 20 420 47 HOH HOH . G 5 HOH A 21 421 46 HOH HOH . G 5 HOH A 22 422 2 HOH HOH . G 5 HOH A 23 423 38 HOH HOH . G 5 HOH A 24 424 29 HOH HOH . G 5 HOH A 25 425 18 HOH HOH . G 5 HOH A 26 426 12 HOH HOH . G 5 HOH A 27 427 25 HOH HOH . G 5 HOH A 28 428 3 HOH HOH . G 5 HOH A 29 429 11 HOH HOH . G 5 HOH A 30 430 22 HOH HOH . G 5 HOH A 31 431 24 HOH HOH . G 5 HOH A 32 432 9 HOH HOH . G 5 HOH A 33 433 36 HOH HOH . G 5 HOH A 34 434 35 HOH HOH . G 5 HOH A 35 435 48 HOH HOH . G 5 HOH A 36 436 37 HOH HOH . G 5 HOH A 37 437 40 HOH HOH . G 5 HOH A 38 438 43 HOH HOH . G 5 HOH A 39 439 31 HOH HOH . G 5 HOH A 40 440 33 HOH HOH . G 5 HOH A 41 441 39 HOH HOH . G 5 HOH A 42 442 42 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 C16 WTS . . . F 4 -1.682 -3.993 0.469 1 18.77 ? C16 WTS 305 A 1 HETATM 2 C C15 WTS . . . F 4 -2.265 -1.56 0.727 1 12.33 ? C15 WTS 305 A 1 HETATM 3 C C14 WTS . . . F 4 -2.386 -2.843 1.111 1 14.02 ? C14 WTS 305 A 1 HETATM 4 C C11 WTS . . . F 4 -3.594 0.254 4.483 1 9.19 ? C11 WTS 305 A 1 HETATM 5 C C10 WTS . . . F 4 -3.839 -1.209 4.179 1 8.47 ? C10 WTS 305 A 1 HETATM 6 C C9 WTS . . . F 4 -3.392 -1.594 2.802 1 12.48 ? C9 WTS 305 A 1 HETATM 7 C C12 WTS . . . F 4 -3.961 1.266 3.684 1 11.1 ? C12 WTS 305 A 1 HETATM 8 C C13 WTS . . . F 4 -3.22 -2.968 2.292 1 8.76 ? C13 WTS 305 A 1 HETATM 9 C C8 WTS . . . F 4 -2.918 -0.604 1.734 1 12.95 ? C8 WTS 305 A 1 HETATM 10 O O1 WTS . . . F 4 -2.892 1.515 0.747 1 10.62 ? O1 WTS 305 A 1 HETATM 11 C C2 WTS . . . F 4 -4.852 0.286 0.061 1 11.37 ? C2 WTS 305 A 1 HETATM 12 C C7 WTS . . . F 4 -3.833 0.544 1.207 1 9.88 ? C7 WTS 305 A 1 HETATM 13 C C6 WTS . . . F 4 -4.675 1.167 2.346 1 11.8 ? C6 WTS 305 A 1 HETATM 14 C C5 WTS . . . F 4 -5.235 2.563 2.038 1 10.82 ? C5 WTS 305 A 1 HETATM 15 C C4 WTS . . . F 4 -5.733 2.706 0.596 1 18.31 ? C4 WTS 305 A 1 HETATM 16 C C3 WTS . . . F 4 -5.494 1.591 -0.424 1 16.05 ? C3 WTS 305 A 1 HETATM 17 C C1 WTS . . . F 4 -4.339 -0.378 -1.214 1 11.5 ? C1 WTS 305 A 1 HETATM 18 C C17 WTS . . . F 4 -2.933 0.584 5.799 1 9.44 ? C17 WTS 305 A 1 HETATM 19 C C18 WTS . . . F 4 -6.749 2.59 1.729 1 8.9 ? C18 WTS 305 A 1 HETATM 20 C C19 WTS . . . F 4 -7.6 1.323 1.84 1 12.4 ? C19 WTS 305 A 1 HETATM 21 C C20 WTS . . . F 4 -7.452 3.893 2.085 1 16.48 ? C20 WTS 305 A 1 HETATM 22 C C21 WTS . . . F 4 -4.535 4.725 -0.216 1 12.67 ? C21 WTS 305 A 1 HETATM 23 C C22 WTS . . . F 4 -4.674 6.156 -0.673 1 24.31 ? C22 WTS 305 A 1 HETATM 24 C C23 WTS . . . F 4 -3.908 6.357 -1.961 1 28.95 ? C23 WTS 305 A 1 HETATM 25 C C24 WTS . . . F 4 -2.548 6.919 -1.618 1 35.05 ? C24 WTS 305 A 1 HETATM 26 C C25 WTS . . . F 4 -6.844 1.773 -2.43 1 18.31 ? C25 WTS 305 A 1 HETATM 27 C C26 WTS . . . F 4 -8.076 1.396 -3.193 1 29.73 ? C26 WTS 305 A 1 HETATM 28 C C27 WTS . . . F 4 -9.131 0.986 -2.185 1 23.06 ? C27 WTS 305 A 1 HETATM 29 C C28 WTS . . . F 4 -9.175 -0.515 -2.083 1 31.13 ? C28 WTS 305 A 1 HETATM 30 O O2 WTS . . . F 4 -4.79 -1.701 2.398 1 12.06 ? O2 WTS 305 A 1 HETATM 31 O O3 WTS . . . F 4 -3.629 -3.999 2.806 1 11.28 ? O3 WTS 305 A 1 HETATM 32 O O4 WTS . . . F 4 -1.626 0.012 5.931 1 10.53 ? O4 WTS 305 A 1 HETATM 33 O O5 WTS . . . F 4 -5.747 4.005 0.058 1 14.91 ? O5 WTS 305 A 1 HETATM 34 O O6 WTS . . . F 4 -3.45 4.177 -0.083 1 19.56 ? O6 WTS 305 A 1 HETATM 35 O O7 WTS . . . F 4 -6.743 1.326 -1.054 1 16.66 ? O7 WTS 305 A 1 HETATM 36 O O8 WTS . . . F 4 -5.946 2.419 -2.936 1 19.14 ? O8 WTS 305 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 36 #