data_1YMG # _model_server_result.job_id unUzsZNUGa4oOgaJzWUqmA _model_server_result.datetime_utc '2025-06-28 02:44:14' _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 1ymg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 1YMG # _exptl.entry_id 1YMG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.395 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'nonyl beta-D-glucopyranoside' _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 1YMG _cell.length_a 110.531 _cell.length_b 110.531 _cell.length_c 53.39 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YMG _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 110.531 0 3 'crystal symmetry operation' 3_555 -y+1/2,x+1/2,z 0 -1 0 1 0 0 0 0 1 55.2655 55.2655 0 4 'crystal symmetry operation' 4_455 y-1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 -55.2655 55.2655 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N # _chem_comp.formula 'C15 H30 O6' _chem_comp.formula_weight 306.395 _chem_comp.id BNG _chem_comp.mon_nstd_flag n _chem_comp.name 'nonyl beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'Beta-NONYLGLUCOSIDE;nonyl beta-D-glucoside;nonyl D-glucoside;nonyl glucoside' # 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 C2 BNG sing 70 n n C1 O1 BNG sing 71 n n C1 O5 BNG sing 72 n n C1 H1 BNG sing 73 n n C2 C3 BNG sing 74 n n C2 O2 BNG sing 75 n n C2 H2 BNG sing 76 n n C3 C4 BNG sing 77 n n C3 O3 BNG sing 78 n n C3 H3 BNG sing 79 n n C4 C5 BNG sing 80 n n C4 O4 BNG sing 81 n n C4 H4 BNG sing 82 n n C5 C6 BNG sing 83 n n C5 O5 BNG sing 84 n n C5 H5 BNG sing 85 n n C6 O6 BNG sing 86 n n C6 H61 BNG sing 87 n n C6 H62 BNG sing 88 n n C1' C2' BNG sing 89 n n C1' O1 BNG sing 90 n n C1' "H1'1" BNG sing 91 n n C1' "H1'2" BNG sing 92 n n C2' C3' BNG sing 93 n n C2' "H2'1" BNG sing 94 n n C2' "H2'2" BNG sing 95 n n C3' C4' BNG sing 96 n n C3' "H3'1" BNG sing 97 n n C3' "H3'2" BNG sing 98 n n C4' C5' BNG sing 99 n n C4' "H4'1" BNG sing 100 n n C4' "H4'2" BNG sing 101 n n C5' C6' BNG sing 102 n n C5' "H5'1" BNG sing 103 n n C5' "H5'2" BNG sing 104 n n C6' C7' BNG sing 105 n n C6' "H6'1" BNG sing 106 n n C6' "H6'2" BNG sing 107 n n C7' C8' BNG sing 108 n n C7' "H7'1" BNG sing 109 n n C7' "H7'2" BNG sing 110 n n C8' C9' BNG sing 111 n n C8' "H8'1" BNG sing 112 n n C8' "H8'2" BNG sing 113 n n C9' "H9'1" BNG sing 114 n n C9' "H9'2" BNG sing 115 n n C9' "H9'3" BNG sing 116 n n O2 HO2 BNG sing 117 n n O3 HO3 BNG sing 118 n n O4 HO4 BNG sing 119 n n O6 HO6 BNG sing 120 n n # _pdbx_chem_comp_identifier.comp_id BNG _pdbx_chem_comp_identifier.identifier b-nonylglucoside _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 1YMG _atom_sites.fract_transf_matrix[1][1] 0.009047 _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] 0.009047 _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] 0.01873 _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 BNG A 1 300 300 BNG BNG . C 2 BNG A 1 301 301 BNG BNG . D 3 HOH A 1 400 400 HOH HOH . D 3 HOH A 2 401 401 HOH HOH . D 3 HOH A 3 402 402 HOH HOH . D 3 HOH A 4 403 403 HOH HOH . D 3 HOH A 5 404 404 HOH HOH . D 3 HOH A 6 405 405 HOH HOH . D 3 HOH A 7 406 406 HOH HOH . D 3 HOH A 8 407 407 HOH HOH . D 3 HOH A 9 408 408 HOH HOH . D 3 HOH A 10 409 409 HOH HOH . D 3 HOH A 11 410 410 HOH HOH . D 3 HOH A 12 411 411 HOH HOH . D 3 HOH A 13 412 412 HOH HOH . D 3 HOH A 14 413 413 HOH HOH . D 3 HOH A 15 414 414 HOH HOH . D 3 HOH A 16 415 415 HOH HOH . D 3 HOH A 17 416 416 HOH HOH . D 3 HOH A 18 417 417 HOH HOH . D 3 HOH A 19 418 418 HOH HOH . D 3 HOH A 20 419 419 HOH HOH . D 3 HOH A 21 420 420 HOH HOH . D 3 HOH A 22 421 421 HOH HOH . D 3 HOH A 23 422 422 HOH HOH . D 3 HOH A 24 423 423 HOH HOH . D 3 HOH A 25 424 424 HOH HOH . D 3 HOH A 26 425 425 HOH HOH . D 3 HOH A 27 426 426 HOH HOH . D 3 HOH A 28 427 427 HOH HOH . D 3 HOH A 29 428 428 HOH HOH . D 3 HOH A 30 429 429 HOH HOH . D 3 HOH A 31 430 430 HOH HOH . D 3 HOH A 32 431 431 HOH HOH . D 3 HOH A 33 432 432 HOH HOH . D 3 HOH A 34 433 433 HOH HOH . D 3 HOH A 35 434 434 HOH HOH . D 3 HOH A 36 435 435 HOH HOH . D 3 HOH A 37 436 436 HOH HOH . D 3 HOH A 38 437 437 HOH HOH . D 3 HOH A 39 438 438 HOH HOH . D 3 HOH A 40 439 439 HOH HOH . D 3 HOH A 41 440 440 HOH HOH . D 3 HOH A 42 441 441 HOH HOH . D 3 HOH A 43 442 442 HOH HOH . D 3 HOH A 44 443 443 HOH HOH . D 3 HOH A 45 444 444 HOH HOH . D 3 HOH A 46 445 445 HOH HOH . D 3 HOH A 47 446 446 HOH HOH . D 3 HOH A 48 447 447 HOH HOH . D 3 HOH A 49 448 448 HOH HOH . D 3 HOH A 50 449 449 HOH HOH . D 3 HOH A 51 450 450 HOH HOH . D 3 HOH A 52 451 451 HOH HOH . D 3 HOH A 53 452 452 HOH HOH . D 3 HOH A 54 453 453 HOH HOH . D 3 HOH A 55 454 454 HOH HOH . D 3 HOH A 56 455 455 HOH HOH . D 3 HOH A 57 456 456 HOH HOH . D 3 HOH A 58 457 457 HOH HOH . D 3 HOH A 59 458 458 HOH HOH . D 3 HOH A 60 459 459 HOH HOH . D 3 HOH A 61 460 460 HOH HOH . D 3 HOH A 62 461 461 HOH HOH . D 3 HOH A 63 462 462 HOH HOH . D 3 HOH A 64 463 463 HOH HOH . D 3 HOH A 65 464 464 HOH HOH . D 3 HOH A 66 465 465 HOH HOH . D 3 HOH A 67 466 466 HOH HOH . D 3 HOH A 68 467 467 HOH HOH . D 3 HOH A 69 468 468 HOH HOH . D 3 HOH A 70 469 469 HOH HOH . D 3 HOH A 71 470 470 HOH HOH . D 3 HOH A 72 471 471 HOH HOH . D 3 HOH A 73 472 472 HOH HOH . D 3 HOH A 74 473 473 HOH HOH . D 3 HOH A 75 474 474 HOH HOH . D 3 HOH A 76 475 475 HOH HOH . D 3 HOH A 77 476 476 HOH HOH . D 3 HOH A 78 477 477 HOH HOH . D 3 HOH A 79 478 478 HOH HOH . D 3 HOH A 80 479 479 HOH HOH . D 3 HOH A 81 480 480 HOH HOH . D 3 HOH A 82 481 481 HOH HOH . D 3 HOH A 83 482 482 HOH HOH . D 3 HOH A 84 483 483 HOH HOH . D 3 HOH A 85 484 484 HOH HOH . D 3 HOH A 86 485 485 HOH HOH . D 3 HOH A 87 486 486 HOH HOH . D 3 HOH A 88 487 487 HOH HOH . D 3 HOH A 89 488 488 HOH HOH . D 3 HOH A 90 489 489 HOH HOH . D 3 HOH A 91 490 490 HOH HOH . D 3 HOH A 92 491 491 HOH HOH . D 3 HOH A 93 492 492 HOH HOH . D 3 HOH A 94 493 493 HOH HOH . D 3 HOH A 95 494 494 HOH HOH . D 3 HOH A 96 495 495 HOH HOH . D 3 HOH A 97 496 496 HOH HOH . D 3 HOH A 98 497 497 HOH HOH . D 3 HOH A 99 498 498 HOH HOH . D 3 HOH A 100 499 499 HOH HOH . D 3 HOH A 101 500 500 HOH HOH . D 3 HOH A 102 501 501 HOH HOH . D 3 HOH A 103 502 502 HOH HOH . D 3 HOH A 104 503 503 HOH HOH . D 3 HOH A 105 504 504 HOH HOH . D 3 HOH A 106 505 505 HOH HOH . D 3 HOH A 107 506 506 HOH HOH . D 3 HOH A 108 507 507 HOH HOH . D 3 HOH A 109 508 508 HOH HOH . D 3 HOH A 110 509 509 HOH HOH . D 3 HOH A 111 510 510 HOH HOH . D 3 HOH A 112 511 511 HOH HOH . D 3 HOH A 113 512 512 HOH HOH . D 3 HOH A 114 513 513 HOH HOH . D 3 HOH A 115 514 514 HOH HOH . D 3 HOH A 116 515 515 HOH HOH . D 3 HOH A 117 516 516 HOH HOH . D 3 HOH A 118 517 517 HOH HOH . D 3 HOH A 119 518 518 HOH HOH . D 3 HOH A 120 519 519 HOH HOH . D 3 HOH A 121 520 520 HOH HOH . D 3 HOH A 122 521 521 HOH HOH . D 3 HOH A 123 522 522 HOH HOH . D 3 HOH A 124 523 523 HOH HOH . D 3 HOH A 125 524 524 HOH HOH . D 3 HOH A 126 525 525 HOH HOH . D 3 HOH A 127 526 526 HOH HOH . D 3 HOH A 128 527 527 HOH HOH . D 3 HOH A 129 528 528 HOH HOH . D 3 HOH A 130 529 529 HOH HOH . D 3 HOH A 131 530 530 HOH HOH . D 3 HOH A 132 531 531 HOH HOH . D 3 HOH A 133 532 532 HOH HOH . D 3 HOH A 134 533 533 HOH HOH . D 3 HOH A 135 534 534 HOH HOH . D 3 HOH A 136 535 535 HOH HOH . D 3 HOH A 137 536 536 HOH HOH . D 3 HOH A 138 537 537 HOH HOH . D 3 HOH A 139 538 538 HOH HOH . D 3 HOH A 140 539 539 HOH HOH . D 3 HOH A 141 540 540 HOH HOH . D 3 HOH A 142 541 541 HOH HOH . D 3 HOH A 143 542 542 HOH HOH . D 3 HOH A 144 543 543 HOH HOH . D 3 HOH A 145 544 544 HOH HOH . D 3 HOH A 146 545 545 HOH HOH . D 3 HOH A 147 546 546 HOH HOH . D 3 HOH A 148 547 547 HOH HOH . D 3 HOH A 149 548 548 HOH HOH . D 3 HOH A 150 549 549 HOH HOH . D 3 HOH A 151 550 550 HOH HOH . D 3 HOH A 152 551 551 HOH HOH . D 3 HOH A 153 552 552 HOH HOH . D 3 HOH A 154 553 553 HOH HOH . D 3 HOH A 155 554 554 HOH HOH . D 3 HOH A 156 555 555 HOH HOH . D 3 HOH A 157 556 556 HOH HOH . D 3 HOH A 158 557 557 HOH HOH . D 3 HOH A 159 558 558 HOH HOH . D 3 HOH A 160 559 559 HOH HOH . D 3 HOH A 161 560 560 HOH HOH . D 3 HOH A 162 561 561 HOH HOH . D 3 HOH A 163 562 562 HOH HOH . D 3 HOH A 164 563 563 HOH HOH . D 3 HOH A 165 564 564 HOH HOH . D 3 HOH A 166 565 565 HOH HOH . D 3 HOH A 167 566 566 HOH HOH . D 3 HOH A 168 567 567 HOH HOH . D 3 HOH A 169 568 568 HOH HOH . D 3 HOH A 170 569 569 HOH HOH . D 3 HOH A 171 570 570 HOH HOH . D 3 HOH A 172 571 571 HOH HOH . D 3 HOH A 173 572 572 HOH HOH . D 3 HOH A 174 573 573 HOH HOH . D 3 HOH A 175 574 574 HOH HOH . D 3 HOH A 176 575 575 HOH HOH . D 3 HOH A 177 576 576 HOH HOH . D 3 HOH A 178 577 577 HOH HOH . D 3 HOH A 179 578 578 HOH HOH . D 3 HOH A 180 579 579 HOH HOH . D 3 HOH A 181 580 580 HOH HOH . D 3 HOH A 182 581 581 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 BNG . . . B 2 -13.344 22.657 55.707 1 67.68 ? C1 BNG 300 A 1 HETATM 2 C C2 BNG . . . B 2 -12.614 21.409 56.375 1 68.14 ? C2 BNG 300 A 1 HETATM 3 C C3 BNG . . . B 2 -13.528 20.807 57.468 1 69.5 ? C3 BNG 300 A 1 HETATM 4 C C4 BNG . . . B 2 -13.781 21.907 58.53 1 70.11 ? C4 BNG 300 A 1 HETATM 5 C C5 BNG . . . B 2 -14.514 23.133 57.827 1 70.34 ? C5 BNG 300 A 1 HETATM 6 C C6 BNG . . . B 2 -14.783 24.243 58.872 1 71.02 ? C6 BNG 300 A 1 HETATM 7 C C1' BNG . . . B 2 -12.769 22.634 53.412 1 66.95 ? C1' BNG 300 A 1 HETATM 8 C C2' BNG . . . B 2 -11.878 23.185 52.293 1 65.8 ? C2' BNG 300 A 1 HETATM 9 C C3' BNG . . . B 2 -12.683 23.992 51.294 1 67.6 ? C3' BNG 300 A 1 HETATM 10 C C4' BNG . . . B 2 -12.912 23.263 49.966 1 68.87 ? C4' BNG 300 A 1 HETATM 11 C C5' BNG . . . B 2 -13.731 24.139 49.023 1 70.11 ? C5' BNG 300 A 1 HETATM 12 C C6' BNG . . . B 2 -13.993 23.481 47.679 1 70.82 ? C6' BNG 300 A 1 HETATM 13 C C7' BNG . . . B 2 -14.813 24.407 46.781 1 72.5 ? C7' BNG 300 A 1 HETATM 14 C C8' BNG . . . B 2 -15.098 23.787 45.422 1 74.25 ? C8' BNG 300 A 1 HETATM 15 C C9' BNG . . . B 2 -15.917 24.755 44.582 1 74.67 ? C9' BNG 300 A 1 HETATM 16 O O1 BNG . . . B 2 -12.489 23.22 54.697 1 65.96 ? O1 BNG 300 A 1 HETATM 17 O O2 BNG . . . B 2 -12.349 20.412 55.373 1 67.23 ? O2 BNG 300 A 1 HETATM 18 O O3 BNG . . . B 2 -12.869 19.675 58.079 1 70.28 ? O3 BNG 300 A 1 HETATM 19 O O4 BNG . . . B 2 -14.621 21.372 59.574 1 73.38 ? O4 BNG 300 A 1 HETATM 20 O O5 BNG . . . B 2 -13.641 23.658 56.751 1 68.28 ? O5 BNG 300 A 1 HETATM 21 O O6 BNG . . . B 2 -15.456 25.368 58.323 1 71.1 ? O6 BNG 300 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #