data_4IMF # _model_server_result.job_id 2AzBi8JJ668Blfpj65zp6g _model_server_result.datetime_utc '2024-11-16 12:29:29' _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 4imf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 4IMF # _exptl.entry_id 4IMF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.27 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid' _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 90 _cell.entry_id 4IMF _cell.length_a 81.71 _cell.length_b 150.23 _cell.length_c 113.09 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4IMF _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 81.71 0 56.545 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 I N N # _chem_comp.formula 'C11 H19 N O9' _chem_comp.formula_weight 309.27 _chem_comp.id SI3 _chem_comp.mon_nstd_flag . _chem_comp.name '5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'N-acetylneuraminic acid, ketone form' # 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 C9 O9 SI3 sing 326 n n C9 C8 SI3 sing 327 n n O7 C7 SI3 sing 328 n n C8 C7 SI3 sing 329 n n C8 O8 SI3 sing 330 n n C7 C6 SI3 sing 331 n n O10 C10 SI3 doub 332 n n O6 C6 SI3 sing 333 n n C6 C5 SI3 sing 334 n n C10 C11 SI3 sing 335 n n C10 N5 SI3 sing 336 n n C5 N5 SI3 sing 337 n n C5 C4 SI3 sing 338 n n O1B C1 SI3 doub 339 n n C4 C3 SI3 sing 340 n n C4 O4 SI3 sing 341 n n C1 O1A SI3 sing 342 n n C1 C2 SI3 sing 343 n n C3 C2 SI3 sing 344 n n C2 O2 SI3 doub 345 n n O1A H1 SI3 sing 346 n n C3 H2 SI3 sing 347 n n C3 H3 SI3 sing 348 n n C4 H4 SI3 sing 349 n n O4 H5 SI3 sing 350 n n C5 H6 SI3 sing 351 n n N5 H7 SI3 sing 352 n n C11 H8 SI3 sing 353 n n C11 H9 SI3 sing 354 n n C11 H10 SI3 sing 355 n n C6 H11 SI3 sing 356 n n O6 H12 SI3 sing 357 n n C7 H13 SI3 sing 358 n n O7 H14 SI3 sing 359 n n C8 H15 SI3 sing 360 n n O8 H16 SI3 sing 361 n n C9 H17 SI3 sing 362 n n C9 H18 SI3 sing 363 n n O9 H19 SI3 sing 364 n n # _atom_sites.entry_id 4IMF _atom_sites.fract_transf_matrix[1][1] 0.012238 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006656 _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] 0.008843 _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 C 2 SI3 A 1 301 500 SI3 SI3 . D 3 ME2 A 1 302 1001 ME2 2PG . E 4 CL A 1 303 2002 CL CL . F 4 CL A 1 304 2003 CL CL . G 5 IPA A 1 305 3001 IPA IPA . H 5 IPA A 1 306 3002 IPA IPA . I 2 SI3 B 1 301 500 SI3 SI3 . J 3 ME2 B 1 302 1002 ME2 2PG . K 3 ME2 B 1 303 1003 ME2 2PG . L 4 CL B 1 304 2001 CL CL . M 6 HOH A 1 401 2 HOH HOH . M 6 HOH A 2 402 4 HOH HOH . M 6 HOH A 3 403 5 HOH HOH . M 6 HOH A 4 404 6 HOH HOH . M 6 HOH A 5 405 9 HOH HOH . M 6 HOH A 6 406 12 HOH HOH . M 6 HOH A 7 407 14 HOH HOH . M 6 HOH A 8 408 16 HOH HOH . M 6 HOH A 9 409 17 HOH HOH . M 6 HOH A 10 410 22 HOH HOH . M 6 HOH A 11 411 23 HOH HOH . M 6 HOH A 12 412 24 HOH HOH . M 6 HOH A 13 413 25 HOH HOH . M 6 HOH A 14 414 26 HOH HOH . M 6 HOH A 15 415 30 HOH HOH . M 6 HOH A 16 416 31 HOH HOH . M 6 HOH A 17 417 32 HOH HOH . M 6 HOH A 18 418 34 HOH HOH . M 6 HOH A 19 419 35 HOH HOH . M 6 HOH A 20 420 38 HOH HOH . M 6 HOH A 21 421 39 HOH HOH . M 6 HOH A 22 422 41 HOH HOH . M 6 HOH A 23 423 43 HOH HOH . M 6 HOH A 24 424 47 HOH HOH . M 6 HOH A 25 425 48 HOH HOH . M 6 HOH A 26 426 51 HOH HOH . M 6 HOH A 27 427 52 HOH HOH . M 6 HOH A 28 428 54 HOH HOH . M 6 HOH A 29 429 57 HOH HOH . M 6 HOH A 30 430 58 HOH HOH . M 6 HOH A 31 431 60 HOH HOH . M 6 HOH A 32 432 62 HOH HOH . M 6 HOH A 33 433 64 HOH HOH . M 6 HOH A 34 434 65 HOH HOH . M 6 HOH A 35 435 67 HOH HOH . M 6 HOH A 36 436 69 HOH HOH . M 6 HOH A 37 437 72 HOH HOH . M 6 HOH A 38 438 76 HOH HOH . M 6 HOH A 39 439 78 HOH HOH . M 6 HOH A 40 440 80 HOH HOH . M 6 HOH A 41 441 81 HOH HOH . M 6 HOH A 42 442 84 HOH HOH . M 6 HOH A 43 443 85 HOH HOH . M 6 HOH A 44 444 86 HOH HOH . M 6 HOH A 45 445 89 HOH HOH . M 6 HOH A 46 446 92 HOH HOH . M 6 HOH A 47 447 93 HOH HOH . M 6 HOH A 48 448 98 HOH HOH . M 6 HOH A 49 449 104 HOH HOH . M 6 HOH A 50 450 106 HOH HOH . M 6 HOH A 51 451 109 HOH HOH . M 6 HOH A 52 452 110 HOH HOH . M 6 HOH A 53 453 111 HOH HOH . M 6 HOH A 54 454 112 HOH HOH . M 6 HOH A 55 455 114 HOH HOH . M 6 HOH A 56 456 117 HOH HOH . M 6 HOH A 57 457 121 HOH HOH . M 6 HOH A 58 458 125 HOH HOH . M 6 HOH A 59 459 126 HOH HOH . M 6 HOH A 60 460 127 HOH HOH . M 6 HOH A 61 461 128 HOH HOH . M 6 HOH A 62 462 129 HOH HOH . M 6 HOH A 63 463 131 HOH HOH . M 6 HOH A 64 464 133 HOH HOH . M 6 HOH A 65 465 134 HOH HOH . M 6 HOH A 66 466 135 HOH HOH . M 6 HOH A 67 467 139 HOH HOH . M 6 HOH A 68 468 143 HOH HOH . M 6 HOH A 69 469 148 HOH HOH . M 6 HOH A 70 470 153 HOH HOH . M 6 HOH A 71 471 155 HOH HOH . M 6 HOH A 72 472 156 HOH HOH . M 6 HOH A 73 473 157 HOH HOH . M 6 HOH A 74 474 160 HOH HOH . M 6 HOH A 75 475 163 HOH HOH . M 6 HOH A 76 476 164 HOH HOH . M 6 HOH A 77 477 165 HOH HOH . M 6 HOH A 78 478 167 HOH HOH . M 6 HOH A 79 479 169 HOH HOH . M 6 HOH A 80 480 173 HOH HOH . M 6 HOH A 81 481 174 HOH HOH . M 6 HOH A 82 482 179 HOH HOH . M 6 HOH A 83 483 181 HOH HOH . M 6 HOH A 84 484 183 HOH HOH . M 6 HOH A 85 485 187 HOH HOH . M 6 HOH A 86 486 188 HOH HOH . M 6 HOH A 87 487 194 HOH HOH . M 6 HOH A 88 488 201 HOH HOH . M 6 HOH A 89 489 202 HOH HOH . M 6 HOH A 90 490 203 HOH HOH . M 6 HOH A 91 491 204 HOH HOH . M 6 HOH A 92 492 207 HOH HOH . M 6 HOH A 93 493 208 HOH HOH . M 6 HOH A 94 494 209 HOH HOH . M 6 HOH A 95 495 210 HOH HOH . M 6 HOH A 96 496 214 HOH HOH . M 6 HOH A 97 497 220 HOH HOH . M 6 HOH A 98 498 221 HOH HOH . M 6 HOH A 99 499 225 HOH HOH . M 6 HOH A 100 500 226 HOH HOH . M 6 HOH A 101 501 227 HOH HOH . M 6 HOH A 102 502 228 HOH HOH . M 6 HOH A 103 503 230 HOH HOH . M 6 HOH A 104 504 231 HOH HOH . M 6 HOH A 105 505 233 HOH HOH . M 6 HOH A 106 506 236 HOH HOH . M 6 HOH A 107 507 241 HOH HOH . M 6 HOH A 108 508 242 HOH HOH . M 6 HOH A 109 509 243 HOH HOH . M 6 HOH A 110 510 244 HOH HOH . M 6 HOH A 111 511 247 HOH HOH . M 6 HOH A 112 512 248 HOH HOH . M 6 HOH A 113 513 252 HOH HOH . M 6 HOH A 114 514 253 HOH HOH . M 6 HOH A 115 515 255 HOH HOH . M 6 HOH A 116 516 256 HOH HOH . M 6 HOH A 117 517 259 HOH HOH . M 6 HOH A 118 518 262 HOH HOH . M 6 HOH A 119 519 263 HOH HOH . M 6 HOH A 120 520 264 HOH HOH . M 6 HOH A 121 521 265 HOH HOH . N 6 HOH B 1 401 1 HOH HOH . N 6 HOH B 2 402 3 HOH HOH . N 6 HOH B 3 403 7 HOH HOH . N 6 HOH B 4 404 8 HOH HOH . N 6 HOH B 5 405 10 HOH HOH . N 6 HOH B 6 406 11 HOH HOH . N 6 HOH B 7 407 13 HOH HOH . N 6 HOH B 8 408 18 HOH HOH . N 6 HOH B 9 409 19 HOH HOH . N 6 HOH B 10 410 20 HOH HOH . N 6 HOH B 11 411 21 HOH HOH . N 6 HOH B 12 412 27 HOH HOH . N 6 HOH B 13 413 28 HOH HOH . N 6 HOH B 14 414 29 HOH HOH . N 6 HOH B 15 415 33 HOH HOH . N 6 HOH B 16 416 36 HOH HOH . N 6 HOH B 17 417 37 HOH HOH . N 6 HOH B 18 418 40 HOH HOH . N 6 HOH B 19 419 42 HOH HOH . N 6 HOH B 20 420 44 HOH HOH . N 6 HOH B 21 421 45 HOH HOH . N 6 HOH B 22 422 46 HOH HOH . N 6 HOH B 23 423 49 HOH HOH . N 6 HOH B 24 424 50 HOH HOH . N 6 HOH B 25 425 53 HOH HOH . N 6 HOH B 26 426 55 HOH HOH . N 6 HOH B 27 427 56 HOH HOH . N 6 HOH B 28 428 59 HOH HOH . N 6 HOH B 29 429 61 HOH HOH . N 6 HOH B 30 430 63 HOH HOH . N 6 HOH B 31 431 66 HOH HOH . N 6 HOH B 32 432 68 HOH HOH . N 6 HOH B 33 433 70 HOH HOH . N 6 HOH B 34 434 71 HOH HOH . N 6 HOH B 35 435 73 HOH HOH . N 6 HOH B 36 436 74 HOH HOH . N 6 HOH B 37 437 77 HOH HOH . N 6 HOH B 38 438 79 HOH HOH . N 6 HOH B 39 439 82 HOH HOH . N 6 HOH B 40 440 83 HOH HOH . N 6 HOH B 41 441 87 HOH HOH . N 6 HOH B 42 442 88 HOH HOH . N 6 HOH B 43 443 90 HOH HOH . N 6 HOH B 44 444 91 HOH HOH . N 6 HOH B 45 445 94 HOH HOH . N 6 HOH B 46 446 95 HOH HOH . N 6 HOH B 47 447 96 HOH HOH . N 6 HOH B 48 448 97 HOH HOH . N 6 HOH B 49 449 99 HOH HOH . N 6 HOH B 50 450 100 HOH HOH . N 6 HOH B 51 451 102 HOH HOH . N 6 HOH B 52 452 103 HOH HOH . N 6 HOH B 53 453 105 HOH HOH . N 6 HOH B 54 454 107 HOH HOH . N 6 HOH B 55 455 108 HOH HOH . N 6 HOH B 56 456 115 HOH HOH . N 6 HOH B 57 457 116 HOH HOH . N 6 HOH B 58 458 118 HOH HOH . N 6 HOH B 59 459 120 HOH HOH . N 6 HOH B 60 460 122 HOH HOH . N 6 HOH B 61 461 123 HOH HOH . N 6 HOH B 62 462 124 HOH HOH . N 6 HOH B 63 463 130 HOH HOH . N 6 HOH B 64 464 132 HOH HOH . N 6 HOH B 65 465 136 HOH HOH . N 6 HOH B 66 466 137 HOH HOH . N 6 HOH B 67 467 138 HOH HOH . N 6 HOH B 68 468 140 HOH HOH . N 6 HOH B 69 469 141 HOH HOH . N 6 HOH B 70 470 142 HOH HOH . N 6 HOH B 71 471 144 HOH HOH . N 6 HOH B 72 472 145 HOH HOH . N 6 HOH B 73 473 146 HOH HOH . N 6 HOH B 74 474 147 HOH HOH . N 6 HOH B 75 475 149 HOH HOH . N 6 HOH B 76 476 150 HOH HOH . N 6 HOH B 77 477 151 HOH HOH . N 6 HOH B 78 478 152 HOH HOH . N 6 HOH B 79 479 154 HOH HOH . N 6 HOH B 80 480 158 HOH HOH . N 6 HOH B 81 481 159 HOH HOH . N 6 HOH B 82 482 161 HOH HOH . N 6 HOH B 83 483 162 HOH HOH . N 6 HOH B 84 484 166 HOH HOH . N 6 HOH B 85 485 168 HOH HOH . N 6 HOH B 86 486 170 HOH HOH . N 6 HOH B 87 487 171 HOH HOH . N 6 HOH B 88 488 172 HOH HOH . N 6 HOH B 89 489 175 HOH HOH . N 6 HOH B 90 490 176 HOH HOH . N 6 HOH B 91 491 177 HOH HOH . N 6 HOH B 92 492 178 HOH HOH . N 6 HOH B 93 493 180 HOH HOH . N 6 HOH B 94 494 182 HOH HOH . N 6 HOH B 95 495 184 HOH HOH . N 6 HOH B 96 496 185 HOH HOH . N 6 HOH B 97 497 186 HOH HOH . N 6 HOH B 98 498 189 HOH HOH . N 6 HOH B 99 499 190 HOH HOH . N 6 HOH B 100 500 191 HOH HOH . N 6 HOH B 101 501 192 HOH HOH . N 6 HOH B 102 502 193 HOH HOH . N 6 HOH B 103 503 195 HOH HOH . N 6 HOH B 104 504 196 HOH HOH . N 6 HOH B 105 505 197 HOH HOH . N 6 HOH B 106 506 198 HOH HOH . N 6 HOH B 107 507 199 HOH HOH . N 6 HOH B 108 508 211 HOH HOH . N 6 HOH B 109 509 212 HOH HOH . N 6 HOH B 110 510 213 HOH HOH . N 6 HOH B 111 511 215 HOH HOH . N 6 HOH B 112 512 216 HOH HOH . N 6 HOH B 113 513 217 HOH HOH . N 6 HOH B 114 514 218 HOH HOH . N 6 HOH B 115 515 219 HOH HOH . N 6 HOH B 116 516 222 HOH HOH . N 6 HOH B 117 517 229 HOH HOH . N 6 HOH B 118 518 232 HOH HOH . N 6 HOH B 119 519 235 HOH HOH . N 6 HOH B 120 520 238 HOH HOH . N 6 HOH B 121 521 239 HOH HOH . N 6 HOH B 122 522 240 HOH HOH . N 6 HOH B 123 523 245 HOH HOH . N 6 HOH B 124 524 246 HOH HOH . N 6 HOH B 125 525 249 HOH HOH . N 6 HOH B 126 526 250 HOH HOH . N 6 HOH B 127 527 251 HOH HOH . N 6 HOH B 128 528 254 HOH HOH . N 6 HOH B 129 529 257 HOH HOH . N 6 HOH B 130 530 258 HOH HOH . N 6 HOH B 131 531 260 HOH HOH . N 6 HOH B 132 532 261 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 O1A SI3 . . . C 2 22.588 27.935 22.882 1 51.16 ? O1A SI3 301 A 1 HETATM 2 C C1 SI3 . . . C 2 23.819 28.116 22.628 1 34.39 ? C1 SI3 301 A 1 HETATM 3 O O1B SI3 . . . C 2 24.06 29.006 21.863 1 47.65 ? O1B SI3 301 A 1 HETATM 4 C C2 SI3 . . . C 2 24.928 27.531 23.27 1 41.99 ? C2 SI3 301 A 1 HETATM 5 O O2 SI3 . . . C 2 25.497 28.291 24.101 1 39.77 ? O2 SI3 301 A 1 HETATM 6 C C3 SI3 . . . C 2 25.291 26.109 22.913 1 35.18 ? C3 SI3 301 A 1 HETATM 7 C C4 SI3 . . . C 2 26.759 25.874 22.622 1 38.8 ? C4 SI3 301 A 1 HETATM 8 O O4 SI3 . . . C 2 27.421 26.321 23.833 1 37.27 ? O4 SI3 301 A 1 HETATM 9 C C5 SI3 . . . C 2 27.283 26.719 21.432 1 31.14 ? C5 SI3 301 A 1 HETATM 10 N N5 SI3 . . . C 2 27.541 28.132 21.846 1 34.87 ? N5 SI3 301 A 1 HETATM 11 C C10 SI3 . . . C 2 27.26 29.183 21.055 1 36.29 ? C10 SI3 301 A 1 HETATM 12 C C11 SI3 . . . C 2 27.332 30.571 21.66 1 32.34 ? C11 SI3 301 A 1 HETATM 13 O O10 SI3 . . . C 2 26.937 28.987 19.841 1 38.51 ? O10 SI3 301 A 1 HETATM 14 C C6 SI3 . . . C 2 28.518 26.044 20.936 1 31.5 ? C6 SI3 301 A 1 HETATM 15 O O6 SI3 . . . C 2 27.981 24.782 20.574 1 32.98 ? O6 SI3 301 A 1 HETATM 16 C C7 SI3 . . . C 2 29.289 26.662 19.747 1 37.04 ? C7 SI3 301 A 1 HETATM 17 O O7 SI3 . . . C 2 28.305 27.053 18.807 1 34.62 ? O7 SI3 301 A 1 HETATM 18 C C8 SI3 . . . C 2 30.319 25.747 19.113 1 36.78 ? C8 SI3 301 A 1 HETATM 19 O O8 SI3 . . . C 2 31.075 25.064 20.165 1 33.11 ? O8 SI3 301 A 1 HETATM 20 C C9 SI3 . . . C 2 31.326 26.429 18.214 1 34.72 ? C9 SI3 301 A 1 HETATM 21 O O9 SI3 . . . C 2 31.888 27.551 18.877 1 34.68 ? O9 SI3 301 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #