data_7UF3 # _model_server_result.job_id jPz-0-rngRqzTm6fwDuW0w _model_server_result.datetime_utc '2024-10-17 19:37:57' _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 7uf3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7UF3 # _exptl.entry_id 7UF3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 230.11 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description L-xylulose-5-phosphate _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 7UF3 _cell.length_a 60.369 _cell.length_b 79.016 _cell.length_c 91.349 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7UF3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 45.6745 # _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 A OE1 GLU 39 A GLU 39 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc2 A OE2 GLU 39 A GLU 39 1_555 D MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc3 A ND1 HIS 154 A HIS 154 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc4 B O05 N3U . A N3U 301 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc5 B O08 N3U . A N3U 301 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc6 B O14 N3U . A N3U 301 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc7 B O05 N3U . A N3U 301 1_555 D MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc8 B O07 N3U . A N3U 301 1_555 D MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc9 C MN MN . A MN 302 1_555 F O HOH . A HOH 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc10 D MN MN . A MN 303 1_555 F O HOH . A HOH 419 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc11 D MN MN . A MN 303 1_555 F O HOH . A HOH 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc12 D MN MN . A MN 303 1_555 F O HOH . A HOH 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? # _chem_comp.formula 'C5 H11 O8 P' _chem_comp.formula_weight 230.11 _chem_comp.id N3U _chem_comp.mon_nstd_flag . _chem_comp.name L-xylulose-5-phosphate _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 O14 P11 N3U doub 237 n n O12 P11 N3U sing 238 n n O13 P11 N3U sing 239 n n P11 O10 N3U sing 240 n n O05 C04 N3U doub 241 n n O10 C01 N3U sing 242 n n O08 C03 N3U sing 243 n n C04 C03 N3U sing 244 n n C04 C06 N3U sing 245 n n O07 C06 N3U sing 246 n n C01 C02 N3U sing 247 n n C03 C02 N3U sing 248 n n C02 O09 N3U sing 249 n n C01 H012 N3U sing 250 n n C01 H011 N3U sing 251 n n C02 H021 N3U sing 252 n n C03 H031 N3U sing 253 n n C06 H061 N3U sing 254 n n C06 H062 N3U sing 255 n n O07 H071 N3U sing 256 n n O08 H081 N3U sing 257 n n O09 H091 N3U sing 258 n n O12 H1 N3U sing 259 n n O13 H2 N3U sing 260 n n # _atom_sites.entry_id 7UF3 _atom_sites.fract_transf_matrix[1][1] 0.016565 _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] 0.012656 _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] 0.010947 _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 N3U A 1 301 1 N3U LIG . C 3 MN A 1 302 1 MN MN . D 3 MN A 1 303 2 MN MN . E 3 MN A 1 304 3 MN MN . F 4 HOH A 1 401 101 HOH HOH . F 4 HOH A 2 402 72 HOH HOH . F 4 HOH A 3 403 102 HOH HOH . F 4 HOH A 4 404 25 HOH HOH . F 4 HOH A 5 405 40 HOH HOH . F 4 HOH A 6 406 46 HOH HOH . F 4 HOH A 7 407 55 HOH HOH . F 4 HOH A 8 408 73 HOH HOH . F 4 HOH A 9 409 52 HOH HOH . F 4 HOH A 10 410 93 HOH HOH . F 4 HOH A 11 411 32 HOH HOH . F 4 HOH A 12 412 8 HOH HOH . F 4 HOH A 13 413 13 HOH HOH . F 4 HOH A 14 414 64 HOH HOH . F 4 HOH A 15 415 15 HOH HOH . F 4 HOH A 16 416 2 HOH HOH . F 4 HOH A 17 417 39 HOH HOH . F 4 HOH A 18 418 14 HOH HOH . F 4 HOH A 19 419 9 HOH HOH . F 4 HOH A 20 420 111 HOH HOH . F 4 HOH A 21 421 69 HOH HOH . F 4 HOH A 22 422 53 HOH HOH . F 4 HOH A 23 423 58 HOH HOH . F 4 HOH A 24 424 34 HOH HOH . F 4 HOH A 25 425 50 HOH HOH . F 4 HOH A 26 426 18 HOH HOH . F 4 HOH A 27 427 85 HOH HOH . F 4 HOH A 28 428 10 HOH HOH . F 4 HOH A 29 429 104 HOH HOH . F 4 HOH A 30 430 1 HOH HOH . F 4 HOH A 31 431 22 HOH HOH . F 4 HOH A 32 432 6 HOH HOH . F 4 HOH A 33 433 43 HOH HOH . F 4 HOH A 34 434 78 HOH HOH . F 4 HOH A 35 435 97 HOH HOH . F 4 HOH A 36 436 3 HOH HOH . F 4 HOH A 37 437 30 HOH HOH . F 4 HOH A 38 438 63 HOH HOH . F 4 HOH A 39 439 48 HOH HOH . F 4 HOH A 40 440 61 HOH HOH . F 4 HOH A 41 441 74 HOH HOH . F 4 HOH A 42 442 16 HOH HOH . F 4 HOH A 43 443 19 HOH HOH . F 4 HOH A 44 444 5 HOH HOH . F 4 HOH A 45 445 11 HOH HOH . F 4 HOH A 46 446 12 HOH HOH . F 4 HOH A 47 447 4 HOH HOH . F 4 HOH A 48 448 119 HOH HOH . F 4 HOH A 49 449 28 HOH HOH . F 4 HOH A 50 450 105 HOH HOH . F 4 HOH A 51 451 36 HOH HOH . F 4 HOH A 52 452 87 HOH HOH . F 4 HOH A 53 453 38 HOH HOH . F 4 HOH A 54 454 29 HOH HOH . F 4 HOH A 55 455 49 HOH HOH . F 4 HOH A 56 456 65 HOH HOH . F 4 HOH A 57 457 62 HOH HOH . F 4 HOH A 58 458 59 HOH HOH . F 4 HOH A 59 459 33 HOH HOH . F 4 HOH A 60 460 24 HOH HOH . F 4 HOH A 61 461 66 HOH HOH . F 4 HOH A 62 462 41 HOH HOH . F 4 HOH A 63 463 100 HOH HOH . F 4 HOH A 64 464 92 HOH HOH . F 4 HOH A 65 465 7 HOH HOH . F 4 HOH A 66 466 75 HOH HOH . F 4 HOH A 67 467 90 HOH HOH . F 4 HOH A 68 468 23 HOH HOH . F 4 HOH A 69 469 31 HOH HOH . F 4 HOH A 70 470 56 HOH HOH . F 4 HOH A 71 471 76 HOH HOH . F 4 HOH A 72 472 83 HOH HOH . F 4 HOH A 73 473 26 HOH HOH . F 4 HOH A 74 474 91 HOH HOH . F 4 HOH A 75 475 94 HOH HOH . F 4 HOH A 76 476 109 HOH HOH . F 4 HOH A 77 477 27 HOH HOH . F 4 HOH A 78 478 54 HOH HOH . F 4 HOH A 79 479 47 HOH HOH . F 4 HOH A 80 480 20 HOH HOH . F 4 HOH A 81 481 103 HOH HOH . F 4 HOH A 82 482 37 HOH HOH . F 4 HOH A 83 483 35 HOH HOH . F 4 HOH A 84 484 21 HOH HOH . F 4 HOH A 85 485 17 HOH HOH . F 4 HOH A 86 486 99 HOH HOH . F 4 HOH A 87 487 118 HOH HOH . F 4 HOH A 88 488 60 HOH HOH . F 4 HOH A 89 489 98 HOH HOH . F 4 HOH A 90 490 80 HOH HOH . F 4 HOH A 91 491 68 HOH HOH . F 4 HOH A 92 492 116 HOH HOH . F 4 HOH A 93 493 110 HOH HOH . F 4 HOH A 94 494 79 HOH HOH . F 4 HOH A 95 495 114 HOH HOH . F 4 HOH A 96 496 84 HOH HOH . F 4 HOH A 97 497 70 HOH HOH . F 4 HOH A 98 498 45 HOH HOH . F 4 HOH A 99 499 67 HOH HOH . F 4 HOH A 100 500 115 HOH HOH . F 4 HOH A 101 501 113 HOH HOH . F 4 HOH A 102 502 57 HOH HOH . F 4 HOH A 103 503 120 HOH HOH . F 4 HOH A 104 504 77 HOH HOH . F 4 HOH A 105 505 71 HOH HOH . F 4 HOH A 106 506 106 HOH HOH . F 4 HOH A 107 507 82 HOH HOH . F 4 HOH A 108 508 122 HOH HOH . F 4 HOH A 109 509 96 HOH HOH . F 4 HOH A 110 510 112 HOH HOH . F 4 HOH A 111 511 121 HOH HOH . F 4 HOH A 112 512 86 HOH HOH . F 4 HOH A 113 513 44 HOH HOH . F 4 HOH A 114 514 42 HOH HOH . F 4 HOH A 115 515 81 HOH HOH . F 4 HOH A 116 516 89 HOH HOH . F 4 HOH A 117 517 108 HOH HOH . F 4 HOH A 118 518 88 HOH HOH . F 4 HOH A 119 519 107 HOH HOH . F 4 HOH A 120 520 117 HOH HOH . F 4 HOH A 121 521 95 HOH HOH . F 4 HOH A 122 522 51 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 C01 N3U . . . B 2 -7.177 -5.199 13.166 1 20 ? C01 N3U 301 A 1 HETATM 2 C C02 N3U . . . B 2 -6.395 -6.041 14.236 1 20 ? C02 N3U 301 A 1 HETATM 3 C C03 N3U . . . B 2 -5.413 -7.065 13.544 1 20 ? C03 N3U 301 A 1 HETATM 4 C C04 N3U . . . B 2 -4.191 -6.406 12.851 1 20 ? C04 N3U 301 A 1 HETATM 5 C C06 N3U . . . B 2 -3.182 -5.524 13.623 1 20 ? C06 N3U 301 A 1 HETATM 6 O O05 N3U . . . B 2 -4.028 -6.554 11.694 1 20 ? O05 N3U 301 A 1 HETATM 7 O O07 N3U . . . B 2 -1.931 -5.389 13.004 1 20 ? O07 N3U 301 A 1 HETATM 8 O O08 N3U . . . B 2 -6.116 -7.839 12.584 1 20 ? O08 N3U 301 A 1 HETATM 9 O O09 N3U . . . B 2 -5.732 -5.24 15.206 1 20 ? O09 N3U 301 A 1 HETATM 10 O O10 N3U . . . B 2 -6.291 -4.545 12.313 1 20 ? O10 N3U 301 A 1 HETATM 11 O O12 N3U . . . B 2 -5.512 -3.532 10.145 1 20 ? O12 N3U 301 A 1 HETATM 12 O O13 N3U . . . B 2 -7.906 -3.671 10.588 1 20 ? O13 N3U 301 A 1 HETATM 13 O O14 N3U . . . B 2 -6.651 -5.686 10.034 1 20 ? O14 N3U 301 A 1 HETATM 14 P P11 N3U . . . B 2 -6.595 -4.367 10.725 1 20 ? P11 N3U 301 A 1 HETATM 15 H H012 N3U . . . B 2 -7.818 -5.851 12.592 1 20 ? H012 N3U 301 A 1 HETATM 16 H H011 N3U . . . B 2 -7.788 -4.464 13.677 1 20 ? H011 N3U 301 A 1 HETATM 17 H H021 N3U . . . B 2 -7.132 -6.628 14.77 1 20 ? H021 N3U 301 A 1 HETATM 18 H H031 N3U . . . B 2 -5.041 -7.737 14.308 1 20 ? H031 N3U 301 A 1 HETATM 19 H H061 N3U . . . B 2 -3.032 -5.956 14.607 1 20 ? H061 N3U 301 A 1 HETATM 20 H H062 N3U . . . B 2 -3.613 -4.536 13.743 1 20 ? H062 N3U 301 A 1 HETATM 21 H H071 N3U . . . B 2 -1.644 -6.231 12.689 1 20 ? H071 N3U 301 A 1 HETATM 22 H H081 N3U . . . B 2 -7.03 -7.875 12.817 1 20 ? H081 N3U 301 A 1 HETATM 23 H H091 N3U . . . B 2 -5.584 -4.377 14.853 1 20 ? H091 N3U 301 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #