data_8YJ9 # _model_server_result.job_id Q60G880GhOQy6bQE4MwVfw _model_server_result.datetime_utc '2025-06-27 21:40:27' _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 8yj9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":304}' # _entry.id 8YJ9 # _exptl.entry_id 8YJ9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description L-ribose _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 8YJ9 _cell.length_a 61.882 _cell.length_b 86.627 _cell.length_c 88.68 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YJ9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _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,J _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _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 A OE2 GLU 8 A GLU 8 1_555 G MN MN . A MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc2 A OD1 ASP 10 A ASP 10 1_555 F CA CA . A CA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc3 A OD2 ASP 10 A ASP 10 1_555 F CA CA . A CA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc4 A OD2 ASP 10 A ASP 10 1_555 G MN MN . A MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc5 A O TYR 12 A TYR 12 1_555 F CA CA . A CA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc6 A OD1 ASN 14 A ASN 14 1_555 F CA CA . A CA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc7 A OD2 ASP 19 A ASP 19 1_555 F CA CA . A CA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc8 A OD1 ASP 19 A ASP 19 1_555 G MN MN . A MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc9 A NE2 HIS 24 A HIS 24 1_555 G MN MN . A MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc10 F CA CA . A CA 305 1_555 J O HOH . A HOH 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc11 F CA CA . A CA 305 1_555 J O HOH . A HOH 462 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc12 G MN MN . A MN 306 1_555 J O HOH . A HOH 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc13 G MN MN . A MN 306 1_555 J O HOH . A HOH 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? # _chem_comp.formula 'C5 H10 O5' _chem_comp.formula_weight 150.13 _chem_comp.id ROR _chem_comp.mon_nstd_flag . _chem_comp.name L-ribose _chem_comp.type l-saccharide _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 O5 C5 ROR sing 277 n n C5 C4 ROR sing 278 n n O4 C4 ROR sing 279 n n C4 C3 ROR sing 280 n n O2 C2 ROR sing 281 n n C3 C2 ROR sing 282 n n C3 O3 ROR sing 283 n n C1 C2 ROR sing 284 n n C1 O1 ROR doub 285 n n C5 H51 ROR sing 286 n n C5 H52 ROR sing 287 n n O5 HO5 ROR sing 288 n n C4 H4 ROR sing 289 n n O4 HO4 ROR sing 290 n n C3 H3 ROR sing 291 n n O3 HO3 ROR sing 292 n n C2 H2 ROR sing 293 n n O2 HO2 ROR sing 294 n n C1 H1 ROR sing 295 n n # _atom_sites.entry_id 8YJ9 _atom_sites.fract_transf_matrix[1][1] 0.01616 _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] 0.011544 _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] 0.011276 _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 GOL A 1 301 301 GOL GOL . C 2 GOL A 1 302 303 GOL GOL . D 2 GOL A 1 303 304 GOL GOL . E 3 ROR A 1 304 305 ROR LIG . F 4 CA A 1 305 1 CA CA . G 5 MN A 1 306 1 MN MN . H 6 SO4 A 1 307 1 SO4 SO4 . I 6 SO4 A 1 308 2 SO4 SO4 . J 7 HOH A 1 401 104 HOH HOH . J 7 HOH A 2 402 191 HOH HOH . J 7 HOH A 3 403 163 HOH HOH . J 7 HOH A 4 404 85 HOH HOH . J 7 HOH A 5 405 14 HOH HOH . J 7 HOH A 6 406 183 HOH HOH . J 7 HOH A 7 407 149 HOH HOH . J 7 HOH A 8 408 17 HOH HOH . J 7 HOH A 9 409 57 HOH HOH . J 7 HOH A 10 410 98 HOH HOH . J 7 HOH A 11 411 75 HOH HOH . J 7 HOH A 12 412 179 HOH HOH . J 7 HOH A 13 413 151 HOH HOH . J 7 HOH A 14 414 159 HOH HOH . J 7 HOH A 15 415 116 HOH HOH . J 7 HOH A 16 416 86 HOH HOH . J 7 HOH A 17 417 42 HOH HOH . J 7 HOH A 18 418 89 HOH HOH . J 7 HOH A 19 419 76 HOH HOH . J 7 HOH A 20 420 72 HOH HOH . J 7 HOH A 21 421 19 HOH HOH . J 7 HOH A 22 422 124 HOH HOH . J 7 HOH A 23 423 181 HOH HOH . J 7 HOH A 24 424 44 HOH HOH . J 7 HOH A 25 425 28 HOH HOH . J 7 HOH A 26 426 2 HOH HOH . J 7 HOH A 27 427 165 HOH HOH . J 7 HOH A 28 428 71 HOH HOH . J 7 HOH A 29 429 61 HOH HOH . J 7 HOH A 30 430 80 HOH HOH . J 7 HOH A 31 431 30 HOH HOH . J 7 HOH A 32 432 66 HOH HOH . J 7 HOH A 33 433 96 HOH HOH . J 7 HOH A 34 434 177 HOH HOH . J 7 HOH A 35 435 189 HOH HOH . J 7 HOH A 36 436 73 HOH HOH . J 7 HOH A 37 437 67 HOH HOH . J 7 HOH A 38 438 37 HOH HOH . J 7 HOH A 39 439 47 HOH HOH . J 7 HOH A 40 440 46 HOH HOH . J 7 HOH A 41 441 43 HOH HOH . J 7 HOH A 42 442 53 HOH HOH . J 7 HOH A 43 443 77 HOH HOH . J 7 HOH A 44 444 92 HOH HOH . J 7 HOH A 45 445 24 HOH HOH . J 7 HOH A 46 446 38 HOH HOH . J 7 HOH A 47 447 187 HOH HOH . J 7 HOH A 48 448 3 HOH HOH . J 7 HOH A 49 449 31 HOH HOH . J 7 HOH A 50 450 27 HOH HOH . J 7 HOH A 51 451 58 HOH HOH . J 7 HOH A 52 452 39 HOH HOH . J 7 HOH A 53 453 35 HOH HOH . J 7 HOH A 54 454 5 HOH HOH . J 7 HOH A 55 455 87 HOH HOH . J 7 HOH A 56 456 142 HOH HOH . J 7 HOH A 57 457 32 HOH HOH . J 7 HOH A 58 458 51 HOH HOH . J 7 HOH A 59 459 33 HOH HOH . J 7 HOH A 60 460 13 HOH HOH . J 7 HOH A 61 461 133 HOH HOH . J 7 HOH A 62 462 4 HOH HOH . J 7 HOH A 63 463 152 HOH HOH . J 7 HOH A 64 464 70 HOH HOH . J 7 HOH A 65 465 106 HOH HOH . J 7 HOH A 66 466 16 HOH HOH . J 7 HOH A 67 467 29 HOH HOH . J 7 HOH A 68 468 11 HOH HOH . J 7 HOH A 69 469 26 HOH HOH . J 7 HOH A 70 470 88 HOH HOH . J 7 HOH A 71 471 36 HOH HOH . J 7 HOH A 72 472 137 HOH HOH . J 7 HOH A 73 473 69 HOH HOH . J 7 HOH A 74 474 95 HOH HOH . J 7 HOH A 75 475 64 HOH HOH . J 7 HOH A 76 476 59 HOH HOH . J 7 HOH A 77 477 40 HOH HOH . J 7 HOH A 78 478 78 HOH HOH . J 7 HOH A 79 479 62 HOH HOH . J 7 HOH A 80 480 91 HOH HOH . J 7 HOH A 81 481 6 HOH HOH . J 7 HOH A 82 482 52 HOH HOH . J 7 HOH A 83 483 182 HOH HOH . J 7 HOH A 84 484 178 HOH HOH . J 7 HOH A 85 485 81 HOH HOH . J 7 HOH A 86 486 65 HOH HOH . J 7 HOH A 87 487 25 HOH HOH . J 7 HOH A 88 488 105 HOH HOH . J 7 HOH A 89 489 8 HOH HOH . J 7 HOH A 90 490 50 HOH HOH . J 7 HOH A 91 491 54 HOH HOH . J 7 HOH A 92 492 15 HOH HOH . J 7 HOH A 93 493 49 HOH HOH . J 7 HOH A 94 494 131 HOH HOH . J 7 HOH A 95 495 173 HOH HOH . J 7 HOH A 96 496 10 HOH HOH . J 7 HOH A 97 497 146 HOH HOH . J 7 HOH A 98 498 41 HOH HOH . J 7 HOH A 99 499 68 HOH HOH . J 7 HOH A 100 500 160 HOH HOH . J 7 HOH A 101 501 171 HOH HOH . J 7 HOH A 102 502 94 HOH HOH . J 7 HOH A 103 503 34 HOH HOH . J 7 HOH A 104 504 83 HOH HOH . J 7 HOH A 105 505 84 HOH HOH . J 7 HOH A 106 506 21 HOH HOH . J 7 HOH A 107 507 90 HOH HOH . J 7 HOH A 108 508 22 HOH HOH . J 7 HOH A 109 509 169 HOH HOH . J 7 HOH A 110 510 82 HOH HOH . J 7 HOH A 111 511 188 HOH HOH . J 7 HOH A 112 512 23 HOH HOH . J 7 HOH A 113 513 150 HOH HOH . J 7 HOH A 114 514 18 HOH HOH . J 7 HOH A 115 515 185 HOH HOH . J 7 HOH A 116 516 20 HOH HOH . J 7 HOH A 117 517 190 HOH HOH . J 7 HOH A 118 518 100 HOH HOH . J 7 HOH A 119 519 186 HOH HOH . J 7 HOH A 120 520 103 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 C5 ROR . . . E 3 17.347 38.8 -3.867 1 23.88 ? C5 ROR 304 A 1 HETATM 2 O O5 ROR . . . E 3 16.095 39.449 -3.672 1 16.73 ? O5 ROR 304 A 1 HETATM 3 C C4 ROR . . . E 3 17.494 38.048 -5.181 1 25.46 ? C4 ROR 304 A 1 HETATM 4 O O4 ROR . . . E 3 17.996 36.801 -4.739 1 24.85 ? O4 ROR 304 A 1 HETATM 5 C C3 ROR . . . E 3 18.482 38.672 -6.192 1 27.67 ? C3 ROR 304 A 1 HETATM 6 O O3 ROR . . . E 3 18.801 39.997 -5.754 1 32.56 ? O3 ROR 304 A 1 HETATM 7 C C2 ROR . . . E 3 18.094 38.841 -7.666 1 24.25 ? C2 ROR 304 A 1 HETATM 8 O O2 ROR . . . E 3 16.756 39.315 -7.688 1 29.79 ? O2 ROR 304 A 1 HETATM 9 C C1 ROR . . . E 3 18.219 37.576 -8.524 1 24.46 ? C1 ROR 304 A 1 HETATM 10 O O1 ROR . . . E 3 17.651 37.393 -9.6 1 19.83 ? O1 ROR 304 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 10 #