data_6XHQ # _model_server_result.job_id Kw-9cx0OUpSoetwPyG2ILw _model_server_result.datetime_utc '2024-12-31 02:35:17' _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 6xhq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 6XHQ # _exptl.entry_id 6XHQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 537.307 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description CDP-ribitol _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 109.26 _cell.angle_gamma 90 _cell.entry_id 6XHQ _cell.length_a 148.935 _cell.length_b 40.057 _cell.length_c 91.823 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XHQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 # _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 ? 2 C N N ? 2 D N N # _chem_comp.formula 'C14 H25 N3 O15 P2' _chem_comp.formula_weight 537.307 _chem_comp.id V2V _chem_comp.mon_nstd_flag . _chem_comp.name CDP-ribitol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4,5-tetrahydroxypentyl dihydrogen diphosphate' # 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 C01 C02 V2V doub 358 n n C01 C07 V2V sing 359 n n C02 N03 V2V sing 360 n n C04 N03 V2V sing 361 n n C04 N06 V2V sing 362 n n C04 O05 V2V doub 363 n n C07 N06 V2V doub 364 n n C07 N08 V2V sing 365 n n C09 C10 V2V sing 366 n n C09 N03 V2V sing 367 n n C09 O13 V2V sing 368 n n C10 C11 V2V sing 369 n n C10 O34 V2V sing 370 n n C11 C12 V2V sing 371 n n C11 O33 V2V sing 372 n n C12 C14 V2V sing 373 n n C14 O15 V2V sing 374 n n C24 C25 V2V sing 375 n n C24 O23 V2V sing 376 n n C25 C26 V2V sing 377 n n C25 O32 V2V sing 378 n n C26 C27 V2V sing 379 n n C26 O31 V2V sing 380 n n C27 C28 V2V sing 381 n n C27 O30 V2V sing 382 n n C28 O29 V2V sing 383 n n O15 P16 V2V sing 384 n n O17 P16 V2V doub 385 n n O18 P16 V2V sing 386 n n O19 P16 V2V sing 387 n n O19 P20 V2V sing 388 n n O21 P20 V2V doub 389 n n O22 P20 V2V sing 390 n n O23 P20 V2V sing 391 n n C01 H1 V2V sing 392 n n C02 H2 V2V sing 393 n n C09 H3 V2V sing 394 n n C10 H4 V2V sing 395 n n C11 H5 V2V sing 396 n n C12 H6 V2V sing 397 n n C14 H8 V2V sing 398 n n C14 H9 V2V sing 399 n n C24 H10 V2V sing 400 n n C24 H11 V2V sing 401 n n C25 H12 V2V sing 402 n n C26 H13 V2V sing 403 n n C27 H14 V2V sing 404 n n C28 H15 V2V sing 405 n n C28 H16 V2V sing 406 n n N08 H17 V2V sing 407 n n N08 H18 V2V sing 408 n n O18 H20 V2V sing 409 n n O22 H21 V2V sing 410 n n O29 H22 V2V sing 411 n n O30 H23 V2V sing 412 n n O31 H24 V2V sing 413 n n O32 H25 V2V sing 414 n n O33 H26 V2V sing 415 n n O34 H27 V2V sing 416 n n C12 O13 V2V sing 417 n n # _atom_sites.entry_id 6XHQ _atom_sites.fract_transf_matrix[1][1] 0.006714 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002346 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024964 _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] 0.011536 _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 C 2 V2V A 1 301 1 V2V CRB . D 2 V2V B 1 301 2 V2V CRB . E 3 HOH A 1 401 122 HOH HOH . E 3 HOH A 2 402 25 HOH HOH . E 3 HOH A 3 403 117 HOH HOH . E 3 HOH A 4 404 110 HOH HOH . E 3 HOH A 5 405 4 HOH HOH . E 3 HOH A 6 406 118 HOH HOH . E 3 HOH A 7 407 67 HOH HOH . E 3 HOH A 8 408 72 HOH HOH . E 3 HOH A 9 409 34 HOH HOH . E 3 HOH A 10 410 78 HOH HOH . E 3 HOH A 11 411 13 HOH HOH . E 3 HOH A 12 412 37 HOH HOH . E 3 HOH A 13 413 105 HOH HOH . E 3 HOH A 14 414 81 HOH HOH . E 3 HOH A 15 415 64 HOH HOH . E 3 HOH A 16 416 75 HOH HOH . E 3 HOH A 17 417 21 HOH HOH . E 3 HOH A 18 418 68 HOH HOH . E 3 HOH A 19 419 3 HOH HOH . E 3 HOH A 20 420 130 HOH HOH . E 3 HOH A 21 421 6 HOH HOH . E 3 HOH A 22 422 47 HOH HOH . E 3 HOH A 23 423 79 HOH HOH . E 3 HOH A 24 424 1 HOH HOH . E 3 HOH A 25 425 50 HOH HOH . E 3 HOH A 26 426 31 HOH HOH . E 3 HOH A 27 427 60 HOH HOH . E 3 HOH A 28 428 2 HOH HOH . E 3 HOH A 29 429 18 HOH HOH . E 3 HOH A 30 430 9 HOH HOH . E 3 HOH A 31 431 20 HOH HOH . E 3 HOH A 32 432 5 HOH HOH . E 3 HOH A 33 433 71 HOH HOH . E 3 HOH A 34 434 69 HOH HOH . E 3 HOH A 35 435 99 HOH HOH . E 3 HOH A 36 436 29 HOH HOH . E 3 HOH A 37 437 43 HOH HOH . E 3 HOH A 38 438 73 HOH HOH . E 3 HOH A 39 439 15 HOH HOH . E 3 HOH A 40 440 106 HOH HOH . E 3 HOH A 41 441 89 HOH HOH . E 3 HOH A 42 442 7 HOH HOH . E 3 HOH A 43 443 36 HOH HOH . E 3 HOH A 44 444 26 HOH HOH . E 3 HOH A 45 445 57 HOH HOH . E 3 HOH A 46 446 39 HOH HOH . E 3 HOH A 47 447 35 HOH HOH . E 3 HOH A 48 448 17 HOH HOH . E 3 HOH A 49 449 88 HOH HOH . E 3 HOH A 50 450 59 HOH HOH . E 3 HOH A 51 451 58 HOH HOH . E 3 HOH A 52 452 121 HOH HOH . E 3 HOH A 53 453 46 HOH HOH . E 3 HOH A 54 454 12 HOH HOH . E 3 HOH A 55 455 42 HOH HOH . E 3 HOH A 56 456 84 HOH HOH . E 3 HOH A 57 457 45 HOH HOH . E 3 HOH A 58 458 28 HOH HOH . E 3 HOH A 59 459 101 HOH HOH . E 3 HOH A 60 460 83 HOH HOH . E 3 HOH A 61 461 49 HOH HOH . E 3 HOH A 62 462 40 HOH HOH . E 3 HOH A 63 463 41 HOH HOH . E 3 HOH A 64 464 123 HOH HOH . E 3 HOH A 65 465 62 HOH HOH . E 3 HOH A 66 466 91 HOH HOH . E 3 HOH A 67 467 56 HOH HOH . E 3 HOH A 68 468 108 HOH HOH . E 3 HOH A 69 469 38 HOH HOH . E 3 HOH A 70 470 138 HOH HOH . E 3 HOH A 71 471 128 HOH HOH . E 3 HOH A 72 472 76 HOH HOH . E 3 HOH A 73 473 139 HOH HOH . E 3 HOH A 74 474 11 HOH HOH . E 3 HOH A 75 475 27 HOH HOH . E 3 HOH A 76 476 100 HOH HOH . E 3 HOH A 77 477 132 HOH HOH . E 3 HOH A 78 478 10 HOH HOH . E 3 HOH A 79 479 86 HOH HOH . E 3 HOH A 80 480 87 HOH HOH . E 3 HOH A 81 481 52 HOH HOH . E 3 HOH A 82 482 96 HOH HOH . E 3 HOH A 83 483 137 HOH HOH . E 3 HOH A 84 484 136 HOH HOH . E 3 HOH A 85 485 48 HOH HOH . E 3 HOH A 86 486 44 HOH HOH . E 3 HOH A 87 487 103 HOH HOH . E 3 HOH A 88 488 54 HOH HOH . E 3 HOH A 89 489 134 HOH HOH . E 3 HOH A 90 490 129 HOH HOH . E 3 HOH A 91 491 93 HOH HOH . E 3 HOH A 92 492 116 HOH HOH . E 3 HOH A 93 493 126 HOH HOH . E 3 HOH A 94 494 77 HOH HOH . E 3 HOH A 95 495 102 HOH HOH . E 3 HOH A 96 496 92 HOH HOH . E 3 HOH A 97 497 112 HOH HOH . E 3 HOH A 98 498 82 HOH HOH . E 3 HOH A 99 499 32 HOH HOH . E 3 HOH A 100 500 24 HOH HOH . F 3 HOH B 1 401 127 HOH HOH . F 3 HOH B 2 402 80 HOH HOH . F 3 HOH B 3 403 16 HOH HOH . F 3 HOH B 4 404 90 HOH HOH . F 3 HOH B 5 405 55 HOH HOH . F 3 HOH B 6 406 19 HOH HOH . F 3 HOH B 7 407 133 HOH HOH . F 3 HOH B 8 408 107 HOH HOH . F 3 HOH B 9 409 66 HOH HOH . F 3 HOH B 10 410 30 HOH HOH . F 3 HOH B 11 411 131 HOH HOH . F 3 HOH B 12 412 53 HOH HOH . F 3 HOH B 13 413 33 HOH HOH . F 3 HOH B 14 414 120 HOH HOH . F 3 HOH B 15 415 23 HOH HOH . F 3 HOH B 16 416 14 HOH HOH . F 3 HOH B 17 417 95 HOH HOH . F 3 HOH B 18 418 135 HOH HOH . F 3 HOH B 19 419 98 HOH HOH . F 3 HOH B 20 420 94 HOH HOH . F 3 HOH B 21 421 8 HOH HOH . F 3 HOH B 22 422 51 HOH HOH . F 3 HOH B 23 423 113 HOH HOH . F 3 HOH B 24 424 115 HOH HOH . F 3 HOH B 25 425 61 HOH HOH . F 3 HOH B 26 426 85 HOH HOH . F 3 HOH B 27 427 111 HOH HOH . F 3 HOH B 28 428 104 HOH HOH . F 3 HOH B 29 429 109 HOH HOH . F 3 HOH B 30 430 114 HOH HOH . F 3 HOH B 31 431 97 HOH HOH . F 3 HOH B 32 432 63 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 V2V . . . D 2 1.363 -16.725 24.805 1 52.23 ? C01 V2V 301 B 1 HETATM 2 C C02 V2V . . . D 2 1.456 -15.355 24.261 1 52.87 ? C02 V2V 301 B 1 HETATM 3 C C04 V2V . . . D 2 3.803 -15.188 25.192 1 53.2 ? C04 V2V 301 B 1 HETATM 4 C C07 V2V . . . D 2 2.488 -17.316 25.542 1 52.6 ? C07 V2V 301 B 1 HETATM 5 C C09 V2V . . . D 2 2.77 -13.221 23.892 1 55.01 ? C09 V2V 301 B 1 HETATM 6 C C10 V2V . . . D 2 2.357 -13.203 22.379 1 54.82 ? C10 V2V 301 B 1 HETATM 7 C C11 V2V . . . D 2 1.863 -11.717 22.171 1 55.04 ? C11 V2V 301 B 1 HETATM 8 C C12 V2V . . . D 2 1.453 -11.305 23.336 1 54.17 ? C12 V2V 301 B 1 HETATM 9 C C14 V2V . . . D 2 -0.05 -11.209 23.396 1 51.54 ? C14 V2V 301 B 1 HETATM 10 C C24 V2V . . . D 2 -2.968 -9.927 25.943 1 51.06 ? C24 V2V 301 B 1 HETATM 11 C C25 V2V . . . D 2 -3.762 -8.697 26.543 1 52.18 ? C25 V2V 301 B 1 HETATM 12 C C26 V2V . . . D 2 -2.86 -7.481 26.648 1 53.73 ? C26 V2V 301 B 1 HETATM 13 C C27 V2V . . . D 2 -3.575 -6.242 27.219 1 54.19 ? C27 V2V 301 B 1 HETATM 14 C C28 V2V . . . D 2 -3.583 -6.24 28.723 1 52.29 ? C28 V2V 301 B 1 HETATM 15 N N03 V2V . . . D 2 2.661 -14.597 24.45 1 53.81 ? N03 V2V 301 B 1 HETATM 16 N N06 V2V . . . D 2 3.7 -16.566 25.74 1 52.66 ? N06 V2V 301 B 1 HETATM 17 N N08 V2V . . . D 2 2.36 -18.676 26.063 1 53.28 ? N08 V2V 301 B 1 HETATM 18 O O05 V2V . . . D 2 4.812 -14.543 25.342 1 53.47 ? O05 V2V 301 B 1 HETATM 19 O O13 V2V . . . D 2 1.946 -12.426 24.487 1 55.27 ? O13 V2V 301 B 1 HETATM 20 O O15 V2V . . . D 2 -0.627 -12.501 23.185 1 49.51 ? O15 V2V 301 B 1 HETATM 21 O O17 V2V . . . D 2 -1.937 -11.662 21.156 1 49.28 ? O17 V2V 301 B 1 HETATM 22 O O18 V2V . . . D 2 -2.502 -13.897 22.003 1 48.62 ? O18 V2V 301 B 1 HETATM 23 O O19 V2V . . . D 2 -3.23 -11.822 23.374 1 50.63 ? O19 V2V 301 B 1 HETATM 24 O O21 V2V . . . D 2 -4.945 -13.153 24.805 1 50.94 ? O21 V2V 301 B 1 HETATM 25 O O22 V2V . . . D 2 -2.576 -13.195 25.528 1 54.65 ? O22 V2V 301 B 1 HETATM 26 O O23 V2V . . . D 2 -3.888 -11.033 25.907 1 51.22 ? O23 V2V 301 B 1 HETATM 27 O O29 V2V . . . D 2 -3.64 -4.888 29.129 1 51.39 ? O29 V2V 301 B 1 HETATM 28 O O30 V2V . . . D 2 -4.904 -6.15 26.737 1 55.98 ? O30 V2V 301 B 1 HETATM 29 O O31 V2V . . . D 2 -2.38 -7.135 25.365 1 54.55 ? O31 V2V 301 B 1 HETATM 30 O O32 V2V . . . D 2 -4.331 -9.029 27.798 1 52.13 ? O32 V2V 301 B 1 HETATM 31 O O33 V2V . . . D 2 2.993 -10.862 21.676 1 55.5 ? O33 V2V 301 B 1 HETATM 32 O O34 V2V . . . D 2 3.397 -13.461 21.597 1 54.5 ? O34 V2V 301 B 1 HETATM 33 P P16 V2V . . . D 2 -2.1 -12.497 22.386 1 49.81 ? P16 V2V 301 B 1 HETATM 34 P P20 V2V . . . D 2 -3.666 -12.331 24.896 1 52.32 ? P20 V2V 301 B 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 34 #