data_5YOI # _model_server_result.job_id aatuNq9I2regcDDYjhN9fA _model_server_result.datetime_utc '2024-10-19 20:15:26' _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 5yoi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":306}' # _entry.id 5YOI # _exptl.entry_id 5YOI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.34 _cell.angle_gamma 90 _cell.entry_id 5YOI _cell.length_a 49.236 _cell.length_b 48.653 _cell.length_c 56.052 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YOI _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,E,F,G,H,I _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 G N N ? 5 H 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 metalc ? metalc1 A O ASN 143 A ASN 109 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc2 A O VAL 145 A VAL 111 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc3 A OD1 ASP 165 A ASP 131 1_555 C CO CO . A CO 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc4 A OD2 ASP 165 A ASP 131 1_555 C CO CO . A CO 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc5 A OD2 ASP 176 A ASP 142 1_555 B CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc6 A OD1 ASP 176 A ASP 142 1_555 C CO CO . A CO 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc7 A NE2 HIS 239 A HIS 205 1_555 B CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc8 A OE2 GLU 272 A GLU 238 1_555 B CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc9 A O THR 299 A THR 265 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc10 A OG1 THR 299 A THR 265 1_555 D NA NA . A NA 303 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc11 A OE1 GLU 303 A GLU 269 1_555 B CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc12 A OE2 GLU 303 A GLU 269 1_555 C CO CO . A CO 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc13 B CO CO . A CO 301 1_555 E OXT MET . A MET 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc14 C CO CO . A CO 302 1_555 E OXT MET . A MET 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc15 C CO CO . A CO 302 1_555 E N MET . A MET 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc16 D NA NA . A NA 303 1_555 I O HOH . A HOH 485 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 O1 GOL sing 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 5YOI _atom_sites.fract_transf_matrix[1][1] 0.02031 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001899 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020554 _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] 0.017918 _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 CO A 1 301 301 CO CO . C 2 CO A 1 302 302 CO CO . D 3 NA A 1 303 311 NA NA . E 4 MET A 1 304 321 MET MET . F 5 GOL A 1 305 331 GOL GOL . G 5 GOL A 1 306 332 GOL GOL . H 5 GOL A 1 307 333 GOL GOL . I 6 HOH A 1 401 542 HOH HOH . I 6 HOH A 2 402 533 HOH HOH . I 6 HOH A 3 403 518 HOH HOH . I 6 HOH A 4 404 400 HOH HOH . I 6 HOH A 5 405 540 HOH HOH . I 6 HOH A 6 406 494 HOH HOH . I 6 HOH A 7 407 399 HOH HOH . I 6 HOH A 8 408 464 HOH HOH . I 6 HOH A 9 409 489 HOH HOH . I 6 HOH A 10 410 480 HOH HOH . I 6 HOH A 11 411 491 HOH HOH . I 6 HOH A 12 412 357 HOH HOH . I 6 HOH A 13 413 455 HOH HOH . I 6 HOH A 14 414 493 HOH HOH . I 6 HOH A 15 415 414 HOH HOH . I 6 HOH A 16 416 536 HOH HOH . I 6 HOH A 17 417 496 HOH HOH . I 6 HOH A 18 418 341 HOH HOH . I 6 HOH A 19 419 396 HOH HOH . I 6 HOH A 20 420 499 HOH HOH . I 6 HOH A 21 421 416 HOH HOH . I 6 HOH A 22 422 462 HOH HOH . I 6 HOH A 23 423 439 HOH HOH . I 6 HOH A 24 424 431 HOH HOH . I 6 HOH A 25 425 474 HOH HOH . I 6 HOH A 26 426 379 HOH HOH . I 6 HOH A 27 427 513 HOH HOH . I 6 HOH A 28 428 381 HOH HOH . I 6 HOH A 29 429 449 HOH HOH . I 6 HOH A 30 430 355 HOH HOH . I 6 HOH A 31 431 421 HOH HOH . I 6 HOH A 32 432 376 HOH HOH . I 6 HOH A 33 433 478 HOH HOH . I 6 HOH A 34 434 467 HOH HOH . I 6 HOH A 35 435 371 HOH HOH . I 6 HOH A 36 436 388 HOH HOH . I 6 HOH A 37 437 470 HOH HOH . I 6 HOH A 38 438 448 HOH HOH . I 6 HOH A 39 439 412 HOH HOH . I 6 HOH A 40 440 405 HOH HOH . I 6 HOH A 41 441 453 HOH HOH . I 6 HOH A 42 442 391 HOH HOH . I 6 HOH A 43 443 353 HOH HOH . I 6 HOH A 44 444 447 HOH HOH . I 6 HOH A 45 445 395 HOH HOH . I 6 HOH A 46 446 393 HOH HOH . I 6 HOH A 47 447 482 HOH HOH . I 6 HOH A 48 448 375 HOH HOH . I 6 HOH A 49 449 488 HOH HOH . I 6 HOH A 50 450 434 HOH HOH . I 6 HOH A 51 451 344 HOH HOH . I 6 HOH A 52 452 530 HOH HOH . I 6 HOH A 53 453 438 HOH HOH . I 6 HOH A 54 454 374 HOH HOH . I 6 HOH A 55 455 524 HOH HOH . I 6 HOH A 56 456 403 HOH HOH . I 6 HOH A 57 457 428 HOH HOH . I 6 HOH A 58 458 492 HOH HOH . I 6 HOH A 59 459 457 HOH HOH . I 6 HOH A 60 460 440 HOH HOH . I 6 HOH A 61 461 445 HOH HOH . I 6 HOH A 62 462 383 HOH HOH . I 6 HOH A 63 463 541 HOH HOH . I 6 HOH A 64 464 419 HOH HOH . I 6 HOH A 65 465 498 HOH HOH . I 6 HOH A 66 466 351 HOH HOH . I 6 HOH A 67 467 365 HOH HOH . I 6 HOH A 68 468 377 HOH HOH . I 6 HOH A 69 469 452 HOH HOH . I 6 HOH A 70 470 460 HOH HOH . I 6 HOH A 71 471 461 HOH HOH . I 6 HOH A 72 472 523 HOH HOH . I 6 HOH A 73 473 472 HOH HOH . I 6 HOH A 74 474 441 HOH HOH . I 6 HOH A 75 475 423 HOH HOH . I 6 HOH A 76 476 354 HOH HOH . I 6 HOH A 77 477 378 HOH HOH . I 6 HOH A 78 478 465 HOH HOH . I 6 HOH A 79 479 473 HOH HOH . I 6 HOH A 80 480 495 HOH HOH . I 6 HOH A 81 481 385 HOH HOH . I 6 HOH A 82 482 520 HOH HOH . I 6 HOH A 83 483 454 HOH HOH . I 6 HOH A 84 484 432 HOH HOH . I 6 HOH A 85 485 515 HOH HOH . I 6 HOH A 86 486 410 HOH HOH . I 6 HOH A 87 487 348 HOH HOH . I 6 HOH A 88 488 413 HOH HOH . I 6 HOH A 89 489 356 HOH HOH . I 6 HOH A 90 490 486 HOH HOH . I 6 HOH A 91 491 418 HOH HOH . I 6 HOH A 92 492 342 HOH HOH . I 6 HOH A 93 493 359 HOH HOH . I 6 HOH A 94 494 437 HOH HOH . I 6 HOH A 95 495 415 HOH HOH . I 6 HOH A 96 496 526 HOH HOH . I 6 HOH A 97 497 497 HOH HOH . I 6 HOH A 98 498 422 HOH HOH . I 6 HOH A 99 499 538 HOH HOH . I 6 HOH A 100 500 537 HOH HOH . I 6 HOH A 101 501 346 HOH HOH . I 6 HOH A 102 502 303 HOH HOH . I 6 HOH A 103 503 384 HOH HOH . I 6 HOH A 104 504 501 HOH HOH . I 6 HOH A 105 505 394 HOH HOH . I 6 HOH A 106 506 468 HOH HOH . I 6 HOH A 107 507 481 HOH HOH . I 6 HOH A 108 508 345 HOH HOH . I 6 HOH A 109 509 517 HOH HOH . I 6 HOH A 110 510 361 HOH HOH . I 6 HOH A 111 511 459 HOH HOH . I 6 HOH A 112 512 430 HOH HOH . I 6 HOH A 113 513 476 HOH HOH . I 6 HOH A 114 514 485 HOH HOH . I 6 HOH A 115 515 304 HOH HOH . I 6 HOH A 116 516 404 HOH HOH . I 6 HOH A 117 517 475 HOH HOH . I 6 HOH A 118 518 367 HOH HOH . I 6 HOH A 119 519 382 HOH HOH . I 6 HOH A 120 520 366 HOH HOH . I 6 HOH A 121 521 364 HOH HOH . I 6 HOH A 122 522 522 HOH HOH . I 6 HOH A 123 523 397 HOH HOH . I 6 HOH A 124 524 372 HOH HOH . I 6 HOH A 125 525 362 HOH HOH . I 6 HOH A 126 526 349 HOH HOH . I 6 HOH A 127 527 398 HOH HOH . I 6 HOH A 128 528 347 HOH HOH . I 6 HOH A 129 529 417 HOH HOH . I 6 HOH A 130 530 425 HOH HOH . I 6 HOH A 131 531 456 HOH HOH . I 6 HOH A 132 532 435 HOH HOH . I 6 HOH A 133 533 444 HOH HOH . I 6 HOH A 134 534 343 HOH HOH . I 6 HOH A 135 535 525 HOH HOH . I 6 HOH A 136 536 380 HOH HOH . I 6 HOH A 137 537 450 HOH HOH . I 6 HOH A 138 538 368 HOH HOH . I 6 HOH A 139 539 543 HOH HOH . I 6 HOH A 140 540 407 HOH HOH . I 6 HOH A 141 541 477 HOH HOH . I 6 HOH A 142 542 424 HOH HOH . I 6 HOH A 143 543 350 HOH HOH . I 6 HOH A 144 544 521 HOH HOH . I 6 HOH A 145 545 532 HOH HOH . I 6 HOH A 146 546 363 HOH HOH . I 6 HOH A 147 547 373 HOH HOH . I 6 HOH A 148 548 369 HOH HOH . I 6 HOH A 149 549 469 HOH HOH . I 6 HOH A 150 550 411 HOH HOH . I 6 HOH A 151 551 544 HOH HOH . I 6 HOH A 152 552 506 HOH HOH . I 6 HOH A 153 553 406 HOH HOH . I 6 HOH A 154 554 433 HOH HOH . I 6 HOH A 155 555 436 HOH HOH . I 6 HOH A 156 556 503 HOH HOH . I 6 HOH A 157 557 502 HOH HOH . I 6 HOH A 158 558 458 HOH HOH . I 6 HOH A 159 559 534 HOH HOH . I 6 HOH A 160 560 463 HOH HOH . I 6 HOH A 161 561 352 HOH HOH . I 6 HOH A 162 562 390 HOH HOH . I 6 HOH A 163 563 360 HOH HOH . I 6 HOH A 164 564 409 HOH HOH . I 6 HOH A 165 565 358 HOH HOH . I 6 HOH A 166 566 408 HOH HOH . I 6 HOH A 167 567 511 HOH HOH . I 6 HOH A 168 568 483 HOH HOH . I 6 HOH A 169 569 389 HOH HOH . I 6 HOH A 170 570 370 HOH HOH . I 6 HOH A 171 571 446 HOH HOH . I 6 HOH A 172 572 507 HOH HOH . I 6 HOH A 173 573 451 HOH HOH . I 6 HOH A 174 574 516 HOH HOH . I 6 HOH A 175 575 531 HOH HOH . I 6 HOH A 176 576 519 HOH HOH . I 6 HOH A 177 577 510 HOH HOH . I 6 HOH A 178 578 471 HOH HOH . I 6 HOH A 179 579 392 HOH HOH . I 6 HOH A 180 580 484 HOH HOH . I 6 HOH A 181 581 505 HOH HOH . I 6 HOH A 182 582 479 HOH HOH . I 6 HOH A 183 583 420 HOH HOH . I 6 HOH A 184 584 426 HOH HOH . I 6 HOH A 185 585 529 HOH HOH . I 6 HOH A 186 586 387 HOH HOH . I 6 HOH A 187 587 500 HOH HOH . I 6 HOH A 188 588 504 HOH HOH . I 6 HOH A 189 589 443 HOH HOH . I 6 HOH A 190 590 528 HOH HOH . I 6 HOH A 191 591 442 HOH HOH . I 6 HOH A 192 592 487 HOH HOH . I 6 HOH A 193 593 509 HOH HOH . I 6 HOH A 194 594 512 HOH HOH . I 6 HOH A 195 595 539 HOH HOH . I 6 HOH A 196 596 466 HOH HOH . I 6 HOH A 197 597 386 HOH HOH . I 6 HOH A 198 598 429 HOH HOH . I 6 HOH A 199 599 508 HOH HOH . I 6 HOH A 200 600 427 HOH HOH . I 6 HOH A 201 601 535 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 GOL . . . G 5 36.964 11.137 14.744 0.5 28.7 ? C1 GOL 306 A 1 HETATM 2 O O1 GOL . . . G 5 36.945 10.658 13.415 0.5 32.83 ? O1 GOL 306 A 1 HETATM 3 C C2 GOL . . . G 5 35.576 11.111 15.283 0.5 29.57 ? C2 GOL 306 A 1 HETATM 4 O O2 GOL . . . G 5 34.766 10.187 14.619 0.5 26.77 ? O2 GOL 306 A 1 HETATM 5 C C3 GOL . . . G 5 34.844 12.379 15.008 0.5 29.98 ? C3 GOL 306 A 1 HETATM 6 O O3 GOL . . . G 5 34.11 12.598 16.199 0.5 30.31 ? O3 GOL 306 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #