data_6MB5 # _model_server_result.job_id lK3qzeWETOe5WWSxNYuJRQ _model_server_result.datetime_utc '2025-02-17 03:14:29' _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 6mb5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6MB5 # _exptl.entry_id 6MB5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 614.644 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NEOMYCIN _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 90 _cell.angle_gamma 120 _cell.entry_id 6MB5 _cell.length_a 106.12 _cell.length_b 106.12 _cell.length_c 68.97 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6MB5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 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 'C23 H46 N6 O13' _chem_comp.formula_weight 614.644 _chem_comp.id NMY _chem_comp.mon_nstd_flag . _chem_comp.name NEOMYCIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms MYCIFRADIN;NEOMAS;PIMAVECORT;VONAMYCIN # 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 O5 NMY sing 224 n n C1 O1 NMY sing 225 n n C1 C2 NMY sing 226 n n C1 H1 NMY sing 227 n n O1 C10 NMY sing 228 n n C2 N2 NMY sing 229 n n C2 C3 NMY sing 230 n n C2 H2 NMY sing 231 n n N2 HN21 NMY sing 232 n n N2 HN22 NMY sing 233 n n C3 C4 NMY sing 234 n n C3 O3 NMY sing 235 n n C3 H3 NMY sing 236 n n O3 HO3 NMY sing 237 n n C4 C5 NMY sing 238 n n C4 O4 NMY sing 239 n n C4 H4 NMY sing 240 n n O4 HO4 NMY sing 241 n n C5 O5 NMY sing 242 n n C5 C6 NMY sing 243 n n C5 H5 NMY sing 244 n n C6 N6 NMY sing 245 n n C6 H61 NMY sing 246 n n C6 H62 NMY sing 247 n n C7 N7 NMY sing 248 n n C7 C12 NMY sing 249 n n C7 C8 NMY sing 250 n n C7 H7 NMY sing 251 n n N7 H71 NMY sing 252 n n N7 H72 NMY sing 253 n n C12 O12 NMY sing 254 n n C12 C11 NMY sing 255 n n C12 H12 NMY sing 256 n n C11 O11 NMY sing 257 n n C11 C10 NMY sing 258 n n C11 H11 NMY sing 259 n n O11 C13 NMY sing 260 n n C10 C9 NMY sing 261 n n C10 H10 NMY sing 262 n n C9 C8 NMY sing 263 n n C9 N9 NMY sing 264 n n C9 H9 NMY sing 265 n n N9 H91 NMY sing 266 n n N9 H92 NMY sing 267 n n C8 H81 NMY sing 268 n n C8 H82 NMY sing 269 n n C13 C14 NMY sing 270 n n C13 O16 NMY sing 271 n n C13 H13 NMY sing 272 n n C14 O14 NMY sing 273 n n C14 C15 NMY sing 274 n n C14 H14 NMY sing 275 n n C15 O18 NMY sing 276 n n C15 C16 NMY sing 277 n n C15 H15 NMY sing 278 n n C16 O16 NMY sing 279 n n C16 C17 NMY sing 280 n n C16 H16 NMY sing 281 n n C17 O17 NMY sing 282 n n C17 H171 NMY sing 283 n n C17 H172 NMY sing 284 n n C21 C20 NMY sing 285 n n C21 C22 NMY sing 286 n n C21 O21 NMY sing 287 n n C21 H21 NMY sing 288 n n C20 C19 NMY sing 289 n n C20 O20 NMY sing 290 n n C20 H20 NMY sing 291 n n C19 N23 NMY sing 292 n n C19 C18 NMY sing 293 n n C19 H19 NMY sing 294 n n C18 O22 NMY sing 295 n n C18 O18 NMY sing 296 n n C18 H18 NMY sing 297 n n C22 O22 NMY sing 298 n n C22 C23 NMY sing 299 n n C22 H22 NMY sing 300 n n C23 N19 NMY sing 301 n n C23 H231 NMY sing 302 n n C23 H232 NMY sing 303 n n N6 HN61 NMY sing 304 n n N6 HN62 NMY sing 305 n n O14 HO41 NMY sing 306 n n O20 HO22 NMY sing 307 n n O21 HO21 NMY sing 308 n n O17 H17 NMY sing 309 n n O12 HO12 NMY sing 310 n n N19 H191 NMY sing 311 n n N19 H192 NMY sing 312 n n N23 HN31 NMY sing 313 n n N23 HN32 NMY sing 314 n n # _atom_sites.entry_id 6MB5 _atom_sites.fract_transf_matrix[1][1] 0.009423 _atom_sites.fract_transf_matrix[1][2] 0.005441 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010881 _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] 0.014499 _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 NMY A 1 301 1 NMY NMY . C 3 HOH A 1 401 114 HOH HOH . C 3 HOH A 2 402 113 HOH HOH . C 3 HOH A 3 403 127 HOH HOH . C 3 HOH A 4 404 34 HOH HOH . C 3 HOH A 5 405 18 HOH HOH . C 3 HOH A 6 406 1 HOH HOH . C 3 HOH A 7 407 16 HOH HOH . C 3 HOH A 8 408 75 HOH HOH . C 3 HOH A 9 409 85 HOH HOH . C 3 HOH A 10 410 131 HOH HOH . C 3 HOH A 11 411 57 HOH HOH . C 3 HOH A 12 412 17 HOH HOH . C 3 HOH A 13 413 3 HOH HOH . C 3 HOH A 14 414 137 HOH HOH . C 3 HOH A 15 415 59 HOH HOH . C 3 HOH A 16 416 112 HOH HOH . C 3 HOH A 17 417 115 HOH HOH . C 3 HOH A 18 418 136 HOH HOH . C 3 HOH A 19 419 77 HOH HOH . C 3 HOH A 20 420 13 HOH HOH . C 3 HOH A 21 421 69 HOH HOH . C 3 HOH A 22 422 54 HOH HOH . C 3 HOH A 23 423 29 HOH HOH . C 3 HOH A 24 424 78 HOH HOH . C 3 HOH A 25 425 8 HOH HOH . C 3 HOH A 26 426 28 HOH HOH . C 3 HOH A 27 427 95 HOH HOH . C 3 HOH A 28 428 128 HOH HOH . C 3 HOH A 29 429 134 HOH HOH . C 3 HOH A 30 430 92 HOH HOH . C 3 HOH A 31 431 93 HOH HOH . C 3 HOH A 32 432 5 HOH HOH . C 3 HOH A 33 433 35 HOH HOH . C 3 HOH A 34 434 2 HOH HOH . C 3 HOH A 35 435 23 HOH HOH . C 3 HOH A 36 436 135 HOH HOH . C 3 HOH A 37 437 27 HOH HOH . C 3 HOH A 38 438 55 HOH HOH . C 3 HOH A 39 439 133 HOH HOH . C 3 HOH A 40 440 14 HOH HOH . C 3 HOH A 41 441 30 HOH HOH . C 3 HOH A 42 442 4 HOH HOH . C 3 HOH A 43 443 10 HOH HOH . C 3 HOH A 44 444 116 HOH HOH . C 3 HOH A 45 445 125 HOH HOH . C 3 HOH A 46 446 11 HOH HOH . C 3 HOH A 47 447 24 HOH HOH . C 3 HOH A 48 448 74 HOH HOH . C 3 HOH A 49 449 21 HOH HOH . C 3 HOH A 50 450 126 HOH HOH . C 3 HOH A 51 451 47 HOH HOH . C 3 HOH A 52 452 130 HOH HOH . C 3 HOH A 53 453 36 HOH HOH . C 3 HOH A 54 454 48 HOH HOH . C 3 HOH A 55 455 51 HOH HOH . C 3 HOH A 56 456 26 HOH HOH . C 3 HOH A 57 457 89 HOH HOH . C 3 HOH A 58 458 32 HOH HOH . C 3 HOH A 59 459 67 HOH HOH . C 3 HOH A 60 460 6 HOH HOH . C 3 HOH A 61 461 31 HOH HOH . C 3 HOH A 62 462 60 HOH HOH . C 3 HOH A 63 463 12 HOH HOH . C 3 HOH A 64 464 98 HOH HOH . C 3 HOH A 65 465 9 HOH HOH . C 3 HOH A 66 466 119 HOH HOH . C 3 HOH A 67 467 37 HOH HOH . C 3 HOH A 68 468 70 HOH HOH . C 3 HOH A 69 469 86 HOH HOH . C 3 HOH A 70 470 7 HOH HOH . C 3 HOH A 71 471 91 HOH HOH . C 3 HOH A 72 472 122 HOH HOH . C 3 HOH A 73 473 111 HOH HOH . C 3 HOH A 74 474 56 HOH HOH . C 3 HOH A 75 475 40 HOH HOH . C 3 HOH A 76 476 84 HOH HOH . C 3 HOH A 77 477 108 HOH HOH . C 3 HOH A 78 478 44 HOH HOH . C 3 HOH A 79 479 22 HOH HOH . C 3 HOH A 80 480 101 HOH HOH . C 3 HOH A 81 481 117 HOH HOH . C 3 HOH A 82 482 39 HOH HOH . C 3 HOH A 83 483 45 HOH HOH . C 3 HOH A 84 484 73 HOH HOH . C 3 HOH A 85 485 15 HOH HOH . C 3 HOH A 86 486 33 HOH HOH . C 3 HOH A 87 487 65 HOH HOH . C 3 HOH A 88 488 76 HOH HOH . C 3 HOH A 89 489 53 HOH HOH . C 3 HOH A 90 490 38 HOH HOH . C 3 HOH A 91 491 61 HOH HOH . C 3 HOH A 92 492 106 HOH HOH . C 3 HOH A 93 493 58 HOH HOH . C 3 HOH A 94 494 96 HOH HOH . C 3 HOH A 95 495 88 HOH HOH . C 3 HOH A 96 496 99 HOH HOH . C 3 HOH A 97 497 118 HOH HOH . C 3 HOH A 98 498 90 HOH HOH . C 3 HOH A 99 499 104 HOH HOH . C 3 HOH A 100 500 83 HOH HOH . C 3 HOH A 101 501 102 HOH HOH . C 3 HOH A 102 502 46 HOH HOH . C 3 HOH A 103 503 120 HOH HOH . C 3 HOH A 104 504 103 HOH HOH . C 3 HOH A 105 505 79 HOH HOH . C 3 HOH A 106 506 110 HOH HOH . C 3 HOH A 107 507 19 HOH HOH . C 3 HOH A 108 508 94 HOH HOH . C 3 HOH A 109 509 49 HOH HOH . C 3 HOH A 110 510 52 HOH HOH . C 3 HOH A 111 511 63 HOH HOH . C 3 HOH A 112 512 82 HOH HOH . C 3 HOH A 113 513 97 HOH HOH . C 3 HOH A 114 514 41 HOH HOH . C 3 HOH A 115 515 80 HOH HOH . C 3 HOH A 116 516 20 HOH HOH . C 3 HOH A 117 517 50 HOH HOH . C 3 HOH A 118 518 25 HOH HOH . C 3 HOH A 119 519 107 HOH HOH . C 3 HOH A 120 520 72 HOH HOH . C 3 HOH A 121 521 66 HOH HOH . C 3 HOH A 122 522 42 HOH HOH . C 3 HOH A 123 523 129 HOH HOH . C 3 HOH A 124 524 71 HOH HOH . C 3 HOH A 125 525 64 HOH HOH . C 3 HOH A 126 526 68 HOH HOH . C 3 HOH A 127 527 87 HOH HOH . C 3 HOH A 128 528 105 HOH HOH . C 3 HOH A 129 529 138 HOH HOH . C 3 HOH A 130 530 100 HOH HOH . C 3 HOH A 131 531 132 HOH HOH . C 3 HOH A 132 532 62 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 C1 NMY . . . B 2 -23.383 -25.906 -16.718 1 48.24 ? C1 NMY 301 A 1 HETATM 2 O O1 NMY . . . B 2 -23.894 -27.09 -16.165 1 47.72 ? O1 NMY 301 A 1 HETATM 3 C C2 NMY . . . B 2 -22.645 -25.186 -15.647 1 48.52 ? C2 NMY 301 A 1 HETATM 4 N N2 NMY . . . B 2 -21.667 -26.164 -14.979 1 51.76 ? N2 NMY 301 A 1 HETATM 5 C C3 NMY . . . B 2 -23.548 -24.66 -14.64 1 49.14 ? C3 NMY 301 A 1 HETATM 6 O O3 NMY . . . B 2 -22.764 -23.98 -13.589 1 50.14 ? O3 NMY 301 A 1 HETATM 7 C C4 NMY . . . B 2 -24.499 -23.695 -15.239 1 49.08 ? C4 NMY 301 A 1 HETATM 8 O O4 NMY . . . B 2 -25.346 -23.18 -14.214 1 49.19 ? O4 NMY 301 A 1 HETATM 9 C C5 NMY . . . B 2 -25.378 -24.354 -16.336 1 48.87 ? C5 NMY 301 A 1 HETATM 10 O O5 NMY . . . B 2 -24.468 -25.104 -17.325 1 47.88 ? O5 NMY 301 A 1 HETATM 11 C C6 NMY . . . B 2 -26.101 -23.343 -17.025 1 48.34 ? C6 NMY 301 A 1 HETATM 12 C C7 NMY . . . B 2 -25.22 -30.749 -17.685 1 43 ? C7 NMY 301 A 1 HETATM 13 N N7 NMY . . . B 2 -25.772 -31.792 -18.543 1 40.75 ? N7 NMY 301 A 1 HETATM 14 C C12 NMY . . . B 2 -23.963 -30.16 -18.348 1 44.61 ? C12 NMY 301 A 1 HETATM 15 C C11 NMY . . . B 2 -23.36 -29.024 -17.519 1 46.59 ? C11 NMY 301 A 1 HETATM 16 O O11 NMY . . . B 2 -22.305 -28.394 -18.268 1 48.14 ? O11 NMY 301 A 1 HETATM 17 C C10 NMY . . . B 2 -24.407 -27.947 -17.161 1 46.13 ? C10 NMY 301 A 1 HETATM 18 C C9 NMY . . . B 2 -25.727 -28.527 -16.616 1 44.17 ? C9 NMY 301 A 1 HETATM 19 N N9 NMY . . . B 2 -26.73 -27.461 -16.571 1 44.12 ? N9 NMY 301 A 1 HETATM 20 C C8 NMY . . . B 2 -26.278 -29.67 -17.463 1 43.18 ? C8 NMY 301 A 1 HETATM 21 C C13 NMY . . . B 2 -21.073 -28.936 -17.984 1 48.87 ? C13 NMY 301 A 1 HETATM 22 C C14 NMY . . . B 2 -20.427 -29.173 -19.131 1 49.31 ? C14 NMY 301 A 1 HETATM 23 C C15 NMY . . . B 2 -19.594 -27.893 -19.354 1 51.75 ? C15 NMY 301 A 1 HETATM 24 C C16 NMY . . . B 2 -19.124 -27.548 -17.883 1 52.16 ? C16 NMY 301 A 1 HETATM 25 O O16 NMY . . . B 2 -20.146 -27.877 -17.125 1 50.16 ? O16 NMY 301 A 1 HETATM 26 C C17 NMY . . . B 2 -18.823 -26.06 -17.738 1 51.52 ? C17 NMY 301 A 1 HETATM 27 C C21 NMY . . . B 2 -17.468 -25.159 -22.921 1 54.48 ? C21 NMY 301 A 1 HETATM 28 C C20 NMY . . . B 2 -17.418 -26.582 -23.35 1 54.06 ? C20 NMY 301 A 1 HETATM 29 C C19 NMY . . . B 2 -17.461 -27.521 -22.204 1 54.19 ? C19 NMY 301 A 1 HETATM 30 C C18 NMY . . . B 2 -18.645 -27.295 -21.332 1 52.96 ? C18 NMY 301 A 1 HETATM 31 O O18 NMY . . . B 2 -18.544 -28.134 -20.173 1 57.28 ? O18 NMY 301 A 1 HETATM 32 C C22 NMY . . . B 2 -18.706 -24.848 -22.041 1 55.22 ? C22 NMY 301 A 1 HETATM 33 O O22 NMY . . . B 2 -18.756 -25.896 -20.884 1 54.37 ? O22 NMY 301 A 1 HETATM 34 C C23 NMY . . . B 2 -18.592 -23.554 -21.492 1 57.09 ? C23 NMY 301 A 1 HETATM 35 N N6 NMY . . . B 2 -27.084 -23.956 -17.904 1 46 ? N6 NMY 301 A 1 HETATM 36 O O14 NMY . . . B 2 -19.541 -30.343 -18.985 1 50.12 ? O14 NMY 301 A 1 HETATM 37 O O20 NMY . . . B 2 -18.564 -26.845 -24.22 1 53.03 ? O20 NMY 301 A 1 HETATM 38 O O21 NMY . . . B 2 -16.284 -24.858 -22.175 1 55.32 ? O21 NMY 301 A 1 HETATM 39 O O17 NMY . . . B 2 -20.024 -25.322 -17.852 1 51.55 ? O17 NMY 301 A 1 HETATM 40 O O12 NMY . . . B 2 -23.038 -31.211 -18.517 1 45.01 ? O12 NMY 301 A 1 HETATM 41 N N19 NMY . . . B 2 -19.595 -23.38 -20.424 1 58.98 ? N19 NMY 301 A 1 HETATM 42 N N23 NMY . . . B 2 -16.202 -27.33 -21.374 1 55.22 ? N23 NMY 301 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 42 #