data_3RYE # _model_server_result.job_id GlUXnsG6PPIbDib3rHecFQ _model_server_result.datetime_utc '2025-01-11 03:52:45' _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 3rye # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":901}' # _entry.id 3RYE # _exptl.entry_id 3RYE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 298.147 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-(2-hydroxy-2,2-diphosphonoethyl)-1-methylpyridinium _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 90 _cell.entry_id 3RYE _cell.length_a 111.311 _cell.length_b 111.311 _cell.length_c 69.713 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RYE _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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,D,E,F,G _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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 34.8565 # _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 # 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 G O HOH . A HOH 3 1_555 E MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc2 A OD1 ASP 99 A ASP 103 1_555 C MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc3 A OD2 ASP 99 A ASP 103 1_555 E MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc4 A OD2 ASP 103 A ASP 107 1_555 C MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc5 A OD2 ASP 103 A ASP 107 1_555 E MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc6 A OD2 ASP 239 A ASP 243 1_555 D MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc7 G O HOH . A HOH 433 1_555 E MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc8 G O HOH . A HOH 476 1_555 D MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc9 G O HOH . A HOH 496 1_555 D MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc10 G O HOH . A HOH 497 1_555 C MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc11 G O HOH . A HOH 499 1_555 D MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc12 G O HOH . A HOH 500 1_555 C MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc13 G O HOH . A HOH 501 1_555 E MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc14 B O9 UNR . A UNR 901 1_555 C MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc15 B O5 UNR . A UNR 901 1_555 C MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc16 B O8 UNR . A UNR 901 1_555 D MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc17 B O6 UNR . A UNR 901 1_555 D MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc18 B O5 UNR . A UNR 901 1_555 E MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? # _chem_comp.formula 'C8 H14 N O7 P2 1' _chem_comp.formula_weight 298.147 _chem_comp.id UNR _chem_comp.mon_nstd_flag . _chem_comp.name 3-(2-hydroxy-2,2-diphosphonoethyl)-1-methylpyridinium _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 C3 C1 UNR sing 362 n n P1 C1 UNR sing 363 n n C1 O2 UNR sing 364 n n C1 P4 UNR sing 365 n n O10 P1 UNR doub 366 n n O9 P1 UNR sing 367 n n P1 O8 UNR sing 368 n n O2 HO2 UNR sing 369 n n C3 C27 UNR sing 370 n n C3 H3 UNR sing 371 n n C3 H3A UNR sing 372 n n O5 P4 UNR doub 373 n n P4 O6 UNR sing 374 n n P4 O7 UNR sing 375 n n O6 HO6 UNR sing 376 n n O7 HO7 UNR sing 377 n n O8 HO8 UNR sing 378 n n O9 HO9 UNR sing 379 n n C27 C17 UNR doub 380 n y C17 C25 UNR sing 381 n y C17 H17 UNR sing 382 n n N26 C18 UNR sing 383 n y C18 C25 UNR doub 384 n y C18 H18 UNR sing 385 n n C22 N26 UNR sing 386 n n C22 H22 UNR sing 387 n n C22 H22A UNR sing 388 n n C22 H22B UNR sing 389 n n C23 N26 UNR doub 390 n y C23 C27 UNR sing 391 n y C23 H23 UNR sing 392 n n C25 H25 UNR sing 393 n n # _atom_sites.entry_id 3RYE _atom_sites.fract_transf_matrix[1][1] 0.008984 _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] 0.008984 _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] 0.014345 _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 UNR A 1 901 901 UNR UNR . C 3 MG A 1 907 907 MG MG . D 3 MG A 1 908 908 MG MG . E 3 MG A 1 909 909 MG MG . F 4 SO4 A 1 1001 1001 SO4 SO4 . G 5 HOH A 1 3 3 HOH HOH . G 5 HOH A 2 4 4 HOH HOH . G 5 HOH A 3 354 5 HOH HOH . G 5 HOH A 4 355 6 HOH HOH . G 5 HOH A 5 356 7 HOH HOH . G 5 HOH A 6 357 8 HOH HOH . G 5 HOH A 7 358 9 HOH HOH . G 5 HOH A 8 359 10 HOH HOH . G 5 HOH A 9 360 11 HOH HOH . G 5 HOH A 10 361 12 HOH HOH . G 5 HOH A 11 362 13 HOH HOH . G 5 HOH A 12 363 14 HOH HOH . G 5 HOH A 13 364 15 HOH HOH . G 5 HOH A 14 365 16 HOH HOH . G 5 HOH A 15 366 17 HOH HOH . G 5 HOH A 16 367 18 HOH HOH . G 5 HOH A 17 368 19 HOH HOH . G 5 HOH A 18 369 20 HOH HOH . G 5 HOH A 19 370 21 HOH HOH . G 5 HOH A 20 371 23 HOH HOH . G 5 HOH A 21 372 24 HOH HOH . G 5 HOH A 22 373 25 HOH HOH . G 5 HOH A 23 374 27 HOH HOH . G 5 HOH A 24 375 28 HOH HOH . G 5 HOH A 25 376 29 HOH HOH . G 5 HOH A 26 377 31 HOH HOH . G 5 HOH A 27 378 32 HOH HOH . G 5 HOH A 28 379 33 HOH HOH . G 5 HOH A 29 380 34 HOH HOH . G 5 HOH A 30 381 35 HOH HOH . G 5 HOH A 31 382 36 HOH HOH . G 5 HOH A 32 383 37 HOH HOH . G 5 HOH A 33 384 38 HOH HOH . G 5 HOH A 34 385 39 HOH HOH . G 5 HOH A 35 386 40 HOH HOH . G 5 HOH A 36 387 41 HOH HOH . G 5 HOH A 37 388 42 HOH HOH . G 5 HOH A 38 389 43 HOH HOH . G 5 HOH A 39 390 44 HOH HOH . G 5 HOH A 40 391 46 HOH HOH . G 5 HOH A 41 392 47 HOH HOH . G 5 HOH A 42 393 48 HOH HOH . G 5 HOH A 43 394 49 HOH HOH . G 5 HOH A 44 395 50 HOH HOH . G 5 HOH A 45 396 51 HOH HOH . G 5 HOH A 46 397 52 HOH HOH . G 5 HOH A 47 398 53 HOH HOH . G 5 HOH A 48 399 54 HOH HOH . G 5 HOH A 49 400 55 HOH HOH . G 5 HOH A 50 401 56 HOH HOH . G 5 HOH A 51 402 57 HOH HOH . G 5 HOH A 52 403 58 HOH HOH . G 5 HOH A 53 404 59 HOH HOH . G 5 HOH A 54 405 60 HOH HOH . G 5 HOH A 55 406 61 HOH HOH . G 5 HOH A 56 407 62 HOH HOH . G 5 HOH A 57 408 63 HOH HOH . G 5 HOH A 58 409 65 HOH HOH . G 5 HOH A 59 410 66 HOH HOH . G 5 HOH A 60 411 67 HOH HOH . G 5 HOH A 61 412 68 HOH HOH . G 5 HOH A 62 413 69 HOH HOH . G 5 HOH A 63 414 70 HOH HOH . G 5 HOH A 64 415 71 HOH HOH . G 5 HOH A 65 416 72 HOH HOH . G 5 HOH A 66 417 73 HOH HOH . G 5 HOH A 67 418 74 HOH HOH . G 5 HOH A 68 419 75 HOH HOH . G 5 HOH A 69 420 76 HOH HOH . G 5 HOH A 70 421 77 HOH HOH . G 5 HOH A 71 422 78 HOH HOH . G 5 HOH A 72 423 80 HOH HOH . G 5 HOH A 73 424 81 HOH HOH . G 5 HOH A 74 425 82 HOH HOH . G 5 HOH A 75 426 83 HOH HOH . G 5 HOH A 76 427 86 HOH HOH . G 5 HOH A 77 428 88 HOH HOH . G 5 HOH A 78 429 89 HOH HOH . G 5 HOH A 79 430 90 HOH HOH . G 5 HOH A 80 431 91 HOH HOH . G 5 HOH A 81 432 92 HOH HOH . G 5 HOH A 82 433 93 HOH HOH . G 5 HOH A 83 434 94 HOH HOH . G 5 HOH A 84 435 95 HOH HOH . G 5 HOH A 85 436 96 HOH HOH . G 5 HOH A 86 437 97 HOH HOH . G 5 HOH A 87 438 98 HOH HOH . G 5 HOH A 88 439 99 HOH HOH . G 5 HOH A 89 440 100 HOH HOH . G 5 HOH A 90 441 101 HOH HOH . G 5 HOH A 91 442 103 HOH HOH . G 5 HOH A 92 443 105 HOH HOH . G 5 HOH A 93 444 107 HOH HOH . G 5 HOH A 94 445 108 HOH HOH . G 5 HOH A 95 446 109 HOH HOH . G 5 HOH A 96 447 110 HOH HOH . G 5 HOH A 97 448 111 HOH HOH . G 5 HOH A 98 449 112 HOH HOH . G 5 HOH A 99 450 113 HOH HOH . G 5 HOH A 100 451 114 HOH HOH . G 5 HOH A 101 452 115 HOH HOH . G 5 HOH A 102 453 116 HOH HOH . G 5 HOH A 103 454 117 HOH HOH . G 5 HOH A 104 455 118 HOH HOH . G 5 HOH A 105 456 119 HOH HOH . G 5 HOH A 106 457 120 HOH HOH . G 5 HOH A 107 458 121 HOH HOH . G 5 HOH A 108 459 122 HOH HOH . G 5 HOH A 109 460 123 HOH HOH . G 5 HOH A 110 461 125 HOH HOH . G 5 HOH A 111 462 126 HOH HOH . G 5 HOH A 112 463 127 HOH HOH . G 5 HOH A 113 464 128 HOH HOH . G 5 HOH A 114 465 129 HOH HOH . G 5 HOH A 115 466 130 HOH HOH . G 5 HOH A 116 467 131 HOH HOH . G 5 HOH A 117 468 132 HOH HOH . G 5 HOH A 118 469 134 HOH HOH . G 5 HOH A 119 470 135 HOH HOH . G 5 HOH A 120 471 136 HOH HOH . G 5 HOH A 121 472 138 HOH HOH . G 5 HOH A 122 473 139 HOH HOH . G 5 HOH A 123 474 140 HOH HOH . G 5 HOH A 124 475 141 HOH HOH . G 5 HOH A 125 476 142 HOH HOH . G 5 HOH A 126 477 143 HOH HOH . G 5 HOH A 127 478 144 HOH HOH . G 5 HOH A 128 479 145 HOH HOH . G 5 HOH A 129 480 146 HOH HOH . G 5 HOH A 130 481 147 HOH HOH . G 5 HOH A 131 482 148 HOH HOH . G 5 HOH A 132 483 149 HOH HOH . G 5 HOH A 133 484 150 HOH HOH . G 5 HOH A 134 485 151 HOH HOH . G 5 HOH A 135 486 152 HOH HOH . G 5 HOH A 136 487 153 HOH HOH . G 5 HOH A 137 488 154 HOH HOH . G 5 HOH A 138 489 155 HOH HOH . G 5 HOH A 139 490 156 HOH HOH . G 5 HOH A 140 491 157 HOH HOH . G 5 HOH A 141 492 159 HOH HOH . G 5 HOH A 142 493 160 HOH HOH . G 5 HOH A 143 494 161 HOH HOH . G 5 HOH A 144 495 163 HOH HOH . G 5 HOH A 145 496 164 HOH HOH . G 5 HOH A 146 497 165 HOH HOH . G 5 HOH A 147 498 167 HOH HOH . G 5 HOH A 148 499 168 HOH HOH . G 5 HOH A 149 500 169 HOH HOH . G 5 HOH A 150 501 170 HOH HOH . G 5 HOH A 151 502 173 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 UNR . . . B 2 15.387 -34.361 26.024 1 34.02 ? C1 UNR 901 A 1 HETATM 2 P P1 UNR . . . B 2 15.658 -35.903 25.088 1 34.37 ? P1 UNR 901 A 1 HETATM 3 O O2 UNR . . . B 2 14.107 -34.47 26.669 1 33.03 ? O2 UNR 901 A 1 HETATM 4 C C3 UNR . . . B 2 15.366 -33.225 25.003 1 37.88 ? C3 UNR 901 A 1 HETATM 5 P P4 UNR . . . B 2 16.667 -34.194 27.314 1 32.06 ? P4 UNR 901 A 1 HETATM 6 O O5 UNR . . . B 2 17.96 -34.033 26.546 1 35.13 ? O5 UNR 901 A 1 HETATM 7 O O6 UNR . . . B 2 16.545 -35.483 28.093 1 29.3 ? O6 UNR 901 A 1 HETATM 8 O O7 UNR . . . B 2 16.417 -32.991 28.198 1 31.55 ? O7 UNR 901 A 1 HETATM 9 O O8 UNR . . . B 2 15.527 -36.989 26.131 1 27.6 ? O8 UNR 901 A 1 HETATM 10 O O9 UNR . . . B 2 17.033 -35.843 24.464 1 29.89 ? O9 UNR 901 A 1 HETATM 11 O O10 UNR . . . B 2 14.652 -35.915 23.986 1 26.73 ? O10 UNR 901 A 1 HETATM 12 C C17 UNR . . . B 2 14.269 -31.608 26.644 1 34.58 ? C17 UNR 901 A 1 HETATM 13 C C18 UNR . . . B 2 14.773 -29.255 26.476 1 37.31 ? C18 UNR 901 A 1 HETATM 14 C C22 UNR . . . B 2 16.284 -28.399 24.782 1 38.87 ? C22 UNR 901 A 1 HETATM 15 C C23 UNR . . . B 2 15.759 -30.754 24.977 1 32.89 ? C23 UNR 901 A 1 HETATM 16 C C25 UNR . . . B 2 14.097 -30.3 27.098 1 34.27 ? C25 UNR 901 A 1 HETATM 17 N N26 UNR . . . B 2 15.583 -29.504 25.436 1 36.78 ? N26 UNR 901 A 1 HETATM 18 C C27 UNR . . . B 2 15.119 -31.84 25.566 1 38.38 ? C27 UNR 901 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 18 #