data_4XDM # _model_server_result.job_id nFsPP2WvJaG7pza8c9aKzQ _model_server_result.datetime_utc '2024-11-16 13:28:17' _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 4xdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4XDM # _exptl.entry_id 4XDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 560.636 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GELDANAMYCIN _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 107.93 _cell.angle_gamma 90 _cell.entry_id 4XDM _cell.length_a 41.4 _cell.length_b 44.63 _cell.length_c 60.16 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XDM _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C29 H40 N2 O9' _chem_comp.formula_weight 560.636 _chem_comp.id GDM _chem_comp.mon_nstd_flag . _chem_comp.name GELDANAMYCIN _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 O1 C1 GDM doub 70 n n O2 C6 GDM sing 71 n n O2 C23 GDM sing 72 n n O3 C7 GDM sing 73 n n O3 C24 GDM sing 74 n n O4 C24 GDM doub 75 n n O5 C11 GDM sing 76 n n O5 HO5 GDM sing 77 n n O6 C12 GDM sing 78 n n O6 C27 GDM sing 79 n n O7 C17 GDM sing 80 n n O7 C29 GDM sing 81 n n O8 C18 GDM doub 82 n n O9 C21 GDM doub 83 n n N1 C1 GDM sing 84 n n N1 C20 GDM sing 85 n n N1 HN1 GDM sing 86 n n N2 C24 GDM sing 87 n n N2 HN21 GDM sing 88 n n N2 HN22 GDM sing 89 n n C1 C2 GDM sing 90 n n C2 C3 GDM doub 91 e n C2 C22 GDM sing 92 n n C3 C4 GDM sing 93 n n C3 H3 GDM sing 94 n n C4 C5 GDM doub 95 z n C4 H4 GDM sing 96 n n C5 C6 GDM sing 97 n n C5 H5 GDM sing 98 n n C6 C7 GDM sing 99 n n C6 H6 GDM sing 100 n n C7 C8 GDM sing 101 n n C7 H7 GDM sing 102 n n C8 C9 GDM doub 103 e n C8 C25 GDM sing 104 n n C9 C10 GDM sing 105 n n C9 H9 GDM sing 106 n n C10 C11 GDM sing 107 n n C10 C26 GDM sing 108 n n C10 H10 GDM sing 109 n n C11 C12 GDM sing 110 n n C11 H11 GDM sing 111 n n C12 C13 GDM sing 112 n n C12 H12 GDM sing 113 n n C13 C14 GDM sing 114 n n C13 H131 GDM sing 115 n n C13 H132 GDM sing 116 n n C14 C15 GDM sing 117 n n C14 C28 GDM sing 118 n n C14 H14 GDM sing 119 n n C15 C16 GDM sing 120 n n C15 H151 GDM sing 121 n n C15 H152 GDM sing 122 n n C16 C17 GDM doub 123 n n C16 C21 GDM sing 124 n n C17 C18 GDM sing 125 n n C18 C19 GDM sing 126 n n C19 C20 GDM doub 127 n n C19 H19 GDM sing 128 n n C20 C21 GDM sing 129 n n C22 H221 GDM sing 130 n n C22 H222 GDM sing 131 n n C22 H223 GDM sing 132 n n C23 H231 GDM sing 133 n n C23 H232 GDM sing 134 n n C23 H233 GDM sing 135 n n C25 H251 GDM sing 136 n n C25 H252 GDM sing 137 n n C25 H253 GDM sing 138 n n C26 H261 GDM sing 139 n n C26 H262 GDM sing 140 n n C26 H263 GDM sing 141 n n C27 H271 GDM sing 142 n n C27 H272 GDM sing 143 n n C27 H273 GDM sing 144 n n C28 H281 GDM sing 145 n n C28 H282 GDM sing 146 n n C28 H283 GDM sing 147 n n C29 H291 GDM sing 148 n n C29 H292 GDM sing 149 n n C29 H293 GDM sing 150 n n # _atom_sites.entry_id 4XDM _atom_sites.fract_transf_matrix[1][1] 0.024155 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007816 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022406 _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] 0.017471 _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 GDM A 1 301 275 GDM GDM . C 3 PEG A 1 302 1 PEG PEG . D 4 HOH A 1 401 86 HOH HOH . D 4 HOH A 2 402 153 HOH HOH . D 4 HOH A 3 403 122 HOH HOH . D 4 HOH A 4 404 158 HOH HOH . D 4 HOH A 5 405 103 HOH HOH . D 4 HOH A 6 406 94 HOH HOH . D 4 HOH A 7 407 39 HOH HOH . D 4 HOH A 8 408 57 HOH HOH . D 4 HOH A 9 409 126 HOH HOH . D 4 HOH A 10 410 71 HOH HOH . D 4 HOH A 11 411 93 HOH HOH . D 4 HOH A 12 412 58 HOH HOH . D 4 HOH A 13 413 97 HOH HOH . D 4 HOH A 14 414 152 HOH HOH . D 4 HOH A 15 415 62 HOH HOH . D 4 HOH A 16 416 108 HOH HOH . D 4 HOH A 17 417 99 HOH HOH . D 4 HOH A 18 418 79 HOH HOH . D 4 HOH A 19 419 162 HOH HOH . D 4 HOH A 20 420 30 HOH HOH . D 4 HOH A 21 421 139 HOH HOH . D 4 HOH A 22 422 68 HOH HOH . D 4 HOH A 23 423 29 HOH HOH . D 4 HOH A 24 424 14 HOH HOH . D 4 HOH A 25 425 28 HOH HOH . D 4 HOH A 26 426 60 HOH HOH . D 4 HOH A 27 427 166 HOH HOH . D 4 HOH A 28 428 132 HOH HOH . D 4 HOH A 29 429 42 HOH HOH . D 4 HOH A 30 430 147 HOH HOH . D 4 HOH A 31 431 47 HOH HOH . D 4 HOH A 32 432 124 HOH HOH . D 4 HOH A 33 433 67 HOH HOH . D 4 HOH A 34 434 87 HOH HOH . D 4 HOH A 35 435 25 HOH HOH . D 4 HOH A 36 436 95 HOH HOH . D 4 HOH A 37 437 164 HOH HOH . D 4 HOH A 38 438 154 HOH HOH . D 4 HOH A 39 439 116 HOH HOH . D 4 HOH A 40 440 119 HOH HOH . D 4 HOH A 41 441 133 HOH HOH . D 4 HOH A 42 442 92 HOH HOH . D 4 HOH A 43 443 109 HOH HOH . D 4 HOH A 44 444 161 HOH HOH . D 4 HOH A 45 445 168 HOH HOH . D 4 HOH A 46 446 54 HOH HOH . D 4 HOH A 47 447 160 HOH HOH . D 4 HOH A 48 448 101 HOH HOH . D 4 HOH A 49 449 159 HOH HOH . D 4 HOH A 50 450 1 HOH HOH . D 4 HOH A 51 451 3 HOH HOH . D 4 HOH A 52 452 5 HOH HOH . D 4 HOH A 53 453 6 HOH HOH . D 4 HOH A 54 454 7 HOH HOH . D 4 HOH A 55 455 8 HOH HOH . D 4 HOH A 56 456 9 HOH HOH . D 4 HOH A 57 457 12 HOH HOH . D 4 HOH A 58 458 15 HOH HOH . D 4 HOH A 59 459 16 HOH HOH . D 4 HOH A 60 460 17 HOH HOH . D 4 HOH A 61 461 18 HOH HOH . D 4 HOH A 62 462 19 HOH HOH . D 4 HOH A 63 463 20 HOH HOH . D 4 HOH A 64 464 21 HOH HOH . D 4 HOH A 65 465 22 HOH HOH . D 4 HOH A 66 466 24 HOH HOH . D 4 HOH A 67 467 26 HOH HOH . D 4 HOH A 68 468 31 HOH HOH . D 4 HOH A 69 469 32 HOH HOH . D 4 HOH A 70 470 34 HOH HOH . D 4 HOH A 71 471 35 HOH HOH . D 4 HOH A 72 472 36 HOH HOH . D 4 HOH A 73 473 37 HOH HOH . D 4 HOH A 74 474 38 HOH HOH . D 4 HOH A 75 475 40 HOH HOH . D 4 HOH A 76 476 41 HOH HOH . D 4 HOH A 77 477 44 HOH HOH . D 4 HOH A 78 478 45 HOH HOH . D 4 HOH A 79 479 46 HOH HOH . D 4 HOH A 80 480 48 HOH HOH . D 4 HOH A 81 481 49 HOH HOH . D 4 HOH A 82 482 50 HOH HOH . D 4 HOH A 83 483 51 HOH HOH . D 4 HOH A 84 484 53 HOH HOH . D 4 HOH A 85 485 55 HOH HOH . D 4 HOH A 86 486 56 HOH HOH . D 4 HOH A 87 487 59 HOH HOH . D 4 HOH A 88 488 63 HOH HOH . D 4 HOH A 89 489 64 HOH HOH . D 4 HOH A 90 490 65 HOH HOH . D 4 HOH A 91 491 66 HOH HOH . D 4 HOH A 92 492 69 HOH HOH . D 4 HOH A 93 493 70 HOH HOH . D 4 HOH A 94 494 72 HOH HOH . D 4 HOH A 95 495 77 HOH HOH . D 4 HOH A 96 496 78 HOH HOH . D 4 HOH A 97 497 80 HOH HOH . D 4 HOH A 98 498 81 HOH HOH . D 4 HOH A 99 499 82 HOH HOH . D 4 HOH A 100 500 83 HOH HOH . D 4 HOH A 101 501 84 HOH HOH . D 4 HOH A 102 502 85 HOH HOH . D 4 HOH A 103 503 88 HOH HOH . D 4 HOH A 104 504 89 HOH HOH . D 4 HOH A 105 505 90 HOH HOH . D 4 HOH A 106 506 91 HOH HOH . D 4 HOH A 107 507 96 HOH HOH . D 4 HOH A 108 508 98 HOH HOH . D 4 HOH A 109 509 100 HOH HOH . D 4 HOH A 110 510 102 HOH HOH . D 4 HOH A 111 511 104 HOH HOH . D 4 HOH A 112 512 105 HOH HOH . D 4 HOH A 113 513 106 HOH HOH . D 4 HOH A 114 514 107 HOH HOH . D 4 HOH A 115 515 110 HOH HOH . D 4 HOH A 116 516 111 HOH HOH . D 4 HOH A 117 517 112 HOH HOH . D 4 HOH A 118 518 113 HOH HOH . D 4 HOH A 119 519 114 HOH HOH . D 4 HOH A 120 520 115 HOH HOH . D 4 HOH A 121 521 118 HOH HOH . D 4 HOH A 122 522 120 HOH HOH . D 4 HOH A 123 523 121 HOH HOH . D 4 HOH A 124 524 123 HOH HOH . D 4 HOH A 125 525 125 HOH HOH . D 4 HOH A 126 526 127 HOH HOH . D 4 HOH A 127 527 128 HOH HOH . D 4 HOH A 128 528 129 HOH HOH . D 4 HOH A 129 529 130 HOH HOH . D 4 HOH A 130 530 131 HOH HOH . D 4 HOH A 131 531 134 HOH HOH . D 4 HOH A 132 532 135 HOH HOH . D 4 HOH A 133 533 141 HOH HOH . D 4 HOH A 134 534 142 HOH HOH . D 4 HOH A 135 535 146 HOH HOH . D 4 HOH A 136 536 150 HOH HOH . D 4 HOH A 137 537 156 HOH HOH . D 4 HOH A 138 538 157 HOH HOH . D 4 HOH A 139 539 163 HOH HOH . D 4 HOH A 140 540 165 HOH HOH . D 4 HOH A 141 541 167 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 O O1 GDM . . . B 2 7.087 14.041 49.112 1 22.46 ? O1 GDM 301 A 1 HETATM 2 O O2 GDM . . . B 2 6.086 10.007 43.894 1 25.6 ? O2 GDM 301 A 1 HETATM 3 O O3 GDM . . . B 2 5.996 7.572 44.825 1 20.93 ? O3 GDM 301 A 1 HETATM 4 O O4 GDM . . . B 2 4.728 6.172 43.511 1 19.88 ? O4 GDM 301 A 1 HETATM 5 O O5 GDM . . . B 2 -0.49 6.985 47.797 1 25.06 ? O5 GDM 301 A 1 HETATM 6 O O6 GDM . . . B 2 -0.941 9.736 47.037 1 24.98 ? O6 GDM 301 A 1 HETATM 7 O O7 GDM . . . B 2 2.454 8.243 50.995 1 29.9 ? O7 GDM 301 A 1 HETATM 8 O O8 GDM . . . B 2 5.208 7.807 50.854 1 31.61 ? O8 GDM 301 A 1 HETATM 9 O O9 GDM . . . B 2 3.476 12.918 50.361 1 27.73 ? O9 GDM 301 A 1 HETATM 10 N N1 GDM . . . B 2 6.238 12.315 50.221 1 23.56 ? N1 GDM 301 A 1 HETATM 11 N N2 GDM . . . B 2 6.964 5.811 43.621 1 19.68 ? N2 GDM 301 A 1 HETATM 12 C C1 GDM . . . B 2 6.275 13.137 49.167 1 23.09 ? C1 GDM 301 A 1 HETATM 13 C C2 GDM . . . B 2 5.336 13.039 48.044 1 24.52 ? C2 GDM 301 A 1 HETATM 14 C C3 GDM . . . B 2 5.173 11.894 47.349 1 23.65 ? C3 GDM 301 A 1 HETATM 15 C C4 GDM . . . B 2 4.231 11.765 46.239 1 24.99 ? C4 GDM 301 A 1 HETATM 16 C C5 GDM . . . B 2 4.307 10.842 45.274 1 23.98 ? C5 GDM 301 A 1 HETATM 17 C C6 GDM . . . B 2 5.408 9.817 45.143 1 23.69 ? C6 GDM 301 A 1 HETATM 18 C C7 GDM . . . B 2 4.854 8.407 44.998 1 20.69 ? C7 GDM 301 A 1 HETATM 19 C C8 GDM . . . B 2 4.053 7.884 46.158 1 21.64 ? C8 GDM 301 A 1 HETATM 20 C C9 GDM . . . B 2 2.739 7.667 45.958 1 21.91 ? C9 GDM 301 A 1 HETATM 21 C C10 GDM . . . B 2 1.802 7.108 47.001 1 23.01 ? C10 GDM 301 A 1 HETATM 22 C C11 GDM . . . B 2 0.396 7.709 46.918 1 23.4 ? C11 GDM 301 A 1 HETATM 23 C C12 GDM . . . B 2 0.369 9.201 47.258 1 23.87 ? C12 GDM 301 A 1 HETATM 24 C C13 GDM . . . B 2 0.791 9.416 48.709 1 23.81 ? C13 GDM 301 A 1 HETATM 25 C C14 GDM . . . B 2 0.75 10.845 49.255 1 24 ? C14 GDM 301 A 1 HETATM 26 C C15 GDM . . . B 2 1.341 10.923 50.69 1 24.65 ? C15 GDM 301 A 1 HETATM 27 C C16 GDM . . . B 2 2.834 10.65 50.663 1 26.16 ? C16 GDM 301 A 1 HETATM 28 C C17 GDM . . . B 2 3.333 9.266 50.793 1 27.16 ? C17 GDM 301 A 1 HETATM 29 C C18 GDM . . . B 2 4.796 8.992 50.73 1 27.45 ? C18 GDM 301 A 1 HETATM 30 C C19 GDM . . . B 2 5.699 10.035 50.548 1 26.79 ? C19 GDM 301 A 1 HETATM 31 C C20 GDM . . . B 2 5.289 11.364 50.412 1 24.83 ? C20 GDM 301 A 1 HETATM 32 C C21 GDM . . . B 2 3.84 11.727 50.471 1 25.73 ? C21 GDM 301 A 1 HETATM 33 C C22 GDM . . . B 2 4.622 14.298 47.67 1 26.07 ? C22 GDM 301 A 1 HETATM 34 C C23 GDM . . . B 2 6.885 11.176 43.836 1 25.95 ? C23 GDM 301 A 1 HETATM 35 C C24 GDM . . . B 2 5.844 6.459 43.933 1 18.31 ? C24 GDM 301 A 1 HETATM 36 C C25 GDM . . . B 2 4.74 7.582 47.468 1 22.33 ? C25 GDM 301 A 1 HETATM 37 C C26 GDM . . . B 2 1.754 5.604 46.789 1 24.5 ? C26 GDM 301 A 1 HETATM 38 C C27 GDM . . . B 2 -1.231 9.995 45.659 1 26.36 ? C27 GDM 301 A 1 HETATM 39 C C28 GDM . . . B 2 1.436 11.797 48.271 1 23.62 ? C28 GDM 301 A 1 HETATM 40 C C29 GDM . . . B 2 2.248 7.829 52.347 1 31.5 ? C29 GDM 301 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 40 #