data_6XHQ
#
_model_server_result.job_id            czQJQwKAQMer3X8r_gb4gA 
_model_server_result.datetime_utc      '2024-12-22 03:18:01' 
_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":"C","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 . . . C 2 -26.254 12.515 20.833 1 30.03 ? C01 V2V 301 A 1 
HETATM 2 C C02 V2V . . . C 2 -25.617 11.477 19.98 1 31.67 ? C02 V2V 301 A 1 
HETATM 3 C C04 V2V . . . C 2 -27.701 11.488 18.516 1 32.24 ? C04 V2V 301 A 1 
HETATM 4 C C07 V2V . . . C 2 -27.606 13.037 20.488 1 28.68 ? C07 V2V 301 A 1 
HETATM 5 C C09 V2V . . . C 2 -25.783 9.955 17.946 1 33.21 ? C09 V2V 301 A 1 
HETATM 6 C C10 V2V . . . C 2 -24.558 10.62 17.21 1 30.72 ? C10 V2V 301 A 1 
HETATM 7 C C11 V2V . . . C 2 -23.697 9.361 16.814 1 32.18 ? C11 V2V 301 A 1 
HETATM 8 C C12 V2V . . . C 2 -24.06 8.412 17.618 1 35.72 ? C12 V2V 301 A 1 
HETATM 9 C C14 V2V . . . C 2 -22.954 8.042 18.54 1 38.02 ? C14 V2V 301 A 1 
HETATM 10 C C24 V2V . . . C 2 -22.328 5.498 21.675 1 32.14 ? C24 V2V 301 A 1 
HETATM 11 C C25 V2V . . . C 2 -21.985 4.009 22.069 1 31.74 ? C25 V2V 301 A 1 
HETATM 12 C C26 V2V . . . C 2 -22.42 3.031 20.997 1 33.17 ? C26 V2V 301 A 1 
HETATM 13 C C27 V2V . . . C 2 -22 1.583 21.318 1 35.27 ? C27 V2V 301 A 1 
HETATM 14 C C28 V2V . . . C 2 -22.91 0.988 22.373 1 37.34 ? C28 V2V 301 A 1 
HETATM 15 N N03 V2V . . . C 2 -26.356 10.976 18.844 1 32.64 ? N03 V2V 301 A 1 
HETATM 16 N N06 V2V . . . C 2 -28.31 12.525 19.362 1 29.62 ? N06 V2V 301 A 1 
HETATM 17 N N08 V2V . . . C 2 -28.251 14.065 21.288 1 28.68 ? N08 V2V 301 A 1 
HETATM 18 O O05 V2V . . . C 2 -28.279 11.065 17.544 1 34.35 ? O05 V2V 301 A 1 
HETATM 19 O O13 V2V . . . C 2 -25.261 8.995 18.637 1 35.28 ? O13 V2V 301 A 1 
HETATM 20 O O15 V2V . . . C 2 -22.716 9.159 19.408 1 38.85 ? O15 V2V 301 A 1 
HETATM 21 O O17 V2V . . . C 2 -20.163 9.155 18.83 1 36.6 ? O17 V2V 301 A 1 
HETATM 22 O O18 V2V . . . C 2 -21.046 10.817 20.427 1 37.13 ? O18 V2V 301 A 1 
HETATM 23 O O19 V2V . . . C 2 -20.821 8.369 21.161 1 37.35 ? O19 V2V 301 A 1 
HETATM 24 O O21 V2V . . . C 2 -21.102 8.624 23.709 1 38.06 ? O21 V2V 301 A 1 
HETATM 25 O O22 V2V . . . C 2 -23.146 8.626 22.312 1 35.58 ? O22 V2V 301 A 1 
HETATM 26 O O23 V2V . . . C 2 -21.745 6.373 22.667 1 34.14 ? O23 V2V 301 A 1 
HETATM 27 O O29 V2V . . . C 2 -23.327 -0.326 22.045 1 38.76 ? O29 V2V 301 A 1 
HETATM 28 O O30 V2V . . . C 2 -20.644 1.538 21.76 1 35.33 ? O30 V2V 301 A 1 
HETATM 29 O O31 V2V . . . C 2 -21.831 3.398 19.763 1 34.23 ? O31 V2V 301 A 1 
HETATM 30 O O32 V2V . . . C 2 -22.527 3.71 23.34 1 31.58 ? O32 V2V 301 A 1 
HETATM 31 O O33 V2V . . . C 2 -23.989 9.027 15.392 1 31.6 ? O33 V2V 301 A 1 
HETATM 32 O O34 V2V . . . C 2 -24.886 11.361 16.16 1 28.41 ? O34 V2V 301 A 1 
HETATM 33 P P16 V2V . . . C 2 -21.142 9.407 19.947 1 37.63 ? P16 V2V 301 A 1 
HETATM 34 P P20 V2V . . . C 2 -21.746 8.027 22.474 1 37.27 ? P20 V2V 301 A 1 
#
_model_server_stats.io_time_ms              35 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           34 
#