data_8XKD
#
_model_server_result.job_id            hDtzSisi3gAPlm7213ya8A 
_model_server_result.datetime_utc      '2025-09-08 12:44:41' 
_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          8xkd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    8XKD 
#
_exptl.entry_id    8XKD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            8XKD 
_cell.length_a            82.6 
_cell.length_b            92.81 
_cell.length_c            71.32 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XKD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 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,H 
_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           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                UDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
N1 C2 UDP sing 397 n n 
N1 C6 UDP sing 398 n n 
N1 C1' UDP sing 399 n n 
C2 N3 UDP sing 400 n n 
C2 O2 UDP doub 401 n n 
N3 C4 UDP sing 402 n n 
N3 HN3 UDP sing 403 n n 
C4 C5 UDP sing 404 n n 
C4 O4 UDP doub 405 n n 
C5 C6 UDP doub 406 n n 
C5 H5 UDP sing 407 n n 
C6 H6 UDP sing 408 n n 
C1' C2' UDP sing 409 n n 
C1' O4' UDP sing 410 n n 
C1' H1' UDP sing 411 n n 
C2' O2' UDP sing 412 n n 
C2' C3' UDP sing 413 n n 
C2' H2' UDP sing 414 n n 
O2' HO2' UDP sing 415 n n 
C3' C4' UDP sing 416 n n 
C3' O3' UDP sing 417 n n 
C3' H3' UDP sing 418 n n 
C4' O4' UDP sing 419 n n 
C4' C5' UDP sing 420 n n 
C4' H4' UDP sing 421 n n 
O3' HO3' UDP sing 422 n n 
C5' O5' UDP sing 423 n n 
C5' "H5'1" UDP sing 424 n n 
C5' "H5'2" UDP sing 425 n n 
O5' PA UDP sing 426 n n 
PA O1A UDP doub 427 n n 
PA O2A UDP sing 428 n n 
PA O3A UDP sing 429 n n 
O2A HOA2 UDP sing 430 n n 
O3A PB UDP sing 431 n n 
PB O1B UDP doub 432 n n 
PB O2B UDP sing 433 n n 
PB O3B UDP sing 434 n n 
O2B HOB2 UDP sing 435 n n 
O3B HOB3 UDP sing 436 n n 
#
_atom_sites.entry_id                     8XKD 
_atom_sites.fract_transf_matrix[1][1]    0.012107 
_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]    0.010775 
_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]    0.014021 
_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 UDP A 1 301 1 UDP UDP . 
D 2 UDP B 1 301 2 UDP UDP . 
E 3 PEG B 1 302 1 PEG PEG . 
F 4 PGE B 1 303 1 PGE PGE . 
G 5 HOH A 1 401 176 HOH HOH . 
G 5 HOH A 2 402 16 HOH HOH . 
G 5 HOH A 3 403 17 HOH HOH . 
G 5 HOH A 4 404 178 HOH HOH . 
G 5 HOH A 5 405 142 HOH HOH . 
G 5 HOH A 6 406 109 HOH HOH . 
G 5 HOH A 7 407 6 HOH HOH . 
G 5 HOH A 8 408 23 HOH HOH . 
G 5 HOH A 9 409 156 HOH HOH . 
G 5 HOH A 10 410 43 HOH HOH . 
G 5 HOH A 11 411 8 HOH HOH . 
G 5 HOH A 12 412 3 HOH HOH . 
G 5 HOH A 13 413 27 HOH HOH . 
G 5 HOH A 14 414 51 HOH HOH . 
G 5 HOH A 15 415 47 HOH HOH . 
G 5 HOH A 16 416 37 HOH HOH . 
G 5 HOH A 17 417 22 HOH HOH . 
G 5 HOH A 18 418 29 HOH HOH . 
G 5 HOH A 19 419 41 HOH HOH . 
G 5 HOH A 20 420 136 HOH HOH . 
G 5 HOH A 21 421 57 HOH HOH . 
G 5 HOH A 22 422 15 HOH HOH . 
G 5 HOH A 23 423 149 HOH HOH . 
G 5 HOH A 24 424 25 HOH HOH . 
G 5 HOH A 25 425 114 HOH HOH . 
G 5 HOH A 26 426 152 HOH HOH . 
G 5 HOH A 27 427 34 HOH HOH . 
G 5 HOH A 28 428 1 HOH HOH . 
G 5 HOH A 29 429 26 HOH HOH . 
G 5 HOH A 30 430 7 HOH HOH . 
G 5 HOH A 31 431 135 HOH HOH . 
G 5 HOH A 32 432 12 HOH HOH . 
G 5 HOH A 33 433 101 HOH HOH . 
G 5 HOH A 34 434 35 HOH HOH . 
G 5 HOH A 35 435 42 HOH HOH . 
G 5 HOH A 36 436 111 HOH HOH . 
G 5 HOH A 37 437 10 HOH HOH . 
G 5 HOH A 38 438 145 HOH HOH . 
G 5 HOH A 39 439 36 HOH HOH . 
G 5 HOH A 40 440 48 HOH HOH . 
G 5 HOH A 41 441 104 HOH HOH . 
G 5 HOH A 42 442 44 HOH HOH . 
G 5 HOH A 43 443 141 HOH HOH . 
G 5 HOH A 44 444 175 HOH HOH . 
G 5 HOH A 45 445 30 HOH HOH . 
G 5 HOH A 46 446 11 HOH HOH . 
G 5 HOH A 47 447 54 HOH HOH . 
G 5 HOH A 48 448 52 HOH HOH . 
G 5 HOH A 49 449 53 HOH HOH . 
G 5 HOH A 50 450 18 HOH HOH . 
G 5 HOH A 51 451 40 HOH HOH . 
G 5 HOH A 52 452 58 HOH HOH . 
G 5 HOH A 53 453 14 HOH HOH . 
G 5 HOH A 54 454 13 HOH HOH . 
G 5 HOH A 55 455 172 HOH HOH . 
G 5 HOH A 56 456 50 HOH HOH . 
G 5 HOH A 57 457 147 HOH HOH . 
G 5 HOH A 58 458 9 HOH HOH . 
G 5 HOH A 59 459 133 HOH HOH . 
G 5 HOH A 60 460 60 HOH HOH . 
G 5 HOH A 61 461 21 HOH HOH . 
G 5 HOH A 62 462 55 HOH HOH . 
G 5 HOH A 63 463 49 HOH HOH . 
G 5 HOH A 64 464 46 HOH HOH . 
G 5 HOH A 65 465 153 HOH HOH . 
G 5 HOH A 66 466 154 HOH HOH . 
G 5 HOH A 67 467 24 HOH HOH . 
G 5 HOH A 68 468 127 HOH HOH . 
G 5 HOH A 69 469 94 HOH HOH . 
G 5 HOH A 70 470 113 HOH HOH . 
G 5 HOH A 71 471 2 HOH HOH . 
G 5 HOH A 72 472 59 HOH HOH . 
G 5 HOH A 73 473 112 HOH HOH . 
G 5 HOH A 74 474 159 HOH HOH . 
G 5 HOH A 75 475 155 HOH HOH . 
G 5 HOH A 76 476 146 HOH HOH . 
G 5 HOH A 77 477 177 HOH HOH . 
G 5 HOH A 78 478 4 HOH HOH . 
G 5 HOH A 79 479 56 HOH HOH . 
G 5 HOH A 80 480 5 HOH HOH . 
G 5 HOH A 81 481 31 HOH HOH . 
G 5 HOH A 82 482 110 HOH HOH . 
G 5 HOH A 83 483 20 HOH HOH . 
G 5 HOH A 84 484 19 HOH HOH . 
G 5 HOH A 85 485 45 HOH HOH . 
G 5 HOH A 86 486 38 HOH HOH . 
G 5 HOH A 87 487 157 HOH HOH . 
G 5 HOH A 88 488 158 HOH HOH . 
G 5 HOH A 89 489 150 HOH HOH . 
G 5 HOH A 90 490 134 HOH HOH . 
G 5 HOH A 91 491 33 HOH HOH . 
G 5 HOH A 92 492 39 HOH HOH . 
G 5 HOH A 93 493 144 HOH HOH . 
G 5 HOH A 94 494 148 HOH HOH . 
G 5 HOH A 95 495 143 HOH HOH . 
H 5 HOH B 1 401 166 HOH HOH . 
H 5 HOH B 2 402 122 HOH HOH . 
H 5 HOH B 3 403 182 HOH HOH . 
H 5 HOH B 4 404 78 HOH HOH . 
H 5 HOH B 5 405 179 HOH HOH . 
H 5 HOH B 6 406 184 HOH HOH . 
H 5 HOH B 7 407 73 HOH HOH . 
H 5 HOH B 8 408 76 HOH HOH . 
H 5 HOH B 9 409 69 HOH HOH . 
H 5 HOH B 10 410 170 HOH HOH . 
H 5 HOH B 11 411 66 HOH HOH . 
H 5 HOH B 12 412 167 HOH HOH . 
H 5 HOH B 13 413 63 HOH HOH . 
H 5 HOH B 14 414 163 HOH HOH . 
H 5 HOH B 15 415 74 HOH HOH . 
H 5 HOH B 16 416 88 HOH HOH . 
H 5 HOH B 17 417 183 HOH HOH . 
H 5 HOH B 18 418 140 HOH HOH . 
H 5 HOH B 19 419 61 HOH HOH . 
H 5 HOH B 20 420 129 HOH HOH . 
H 5 HOH B 21 421 117 HOH HOH . 
H 5 HOH B 22 422 162 HOH HOH . 
H 5 HOH B 23 423 85 HOH HOH . 
H 5 HOH B 24 424 115 HOH HOH . 
H 5 HOH B 25 425 161 HOH HOH . 
H 5 HOH B 26 426 118 HOH HOH . 
H 5 HOH B 27 427 91 HOH HOH . 
H 5 HOH B 28 428 82 HOH HOH . 
H 5 HOH B 29 429 107 HOH HOH . 
H 5 HOH B 30 430 151 HOH HOH . 
H 5 HOH B 31 431 32 HOH HOH . 
H 5 HOH B 32 432 123 HOH HOH . 
H 5 HOH B 33 433 171 HOH HOH . 
H 5 HOH B 34 434 72 HOH HOH . 
H 5 HOH B 35 435 102 HOH HOH . 
H 5 HOH B 36 436 139 HOH HOH . 
H 5 HOH B 37 437 128 HOH HOH . 
H 5 HOH B 38 438 103 HOH HOH . 
H 5 HOH B 39 439 89 HOH HOH . 
H 5 HOH B 40 440 71 HOH HOH . 
H 5 HOH B 41 441 97 HOH HOH . 
H 5 HOH B 42 442 87 HOH HOH . 
H 5 HOH B 43 443 98 HOH HOH . 
H 5 HOH B 44 444 108 HOH HOH . 
H 5 HOH B 45 445 68 HOH HOH . 
H 5 HOH B 46 446 81 HOH HOH . 
H 5 HOH B 47 447 96 HOH HOH . 
H 5 HOH B 48 448 70 HOH HOH . 
H 5 HOH B 49 449 120 HOH HOH . 
H 5 HOH B 50 450 80 HOH HOH . 
H 5 HOH B 51 451 92 HOH HOH . 
H 5 HOH B 52 452 131 HOH HOH . 
H 5 HOH B 53 453 77 HOH HOH . 
H 5 HOH B 54 454 165 HOH HOH . 
H 5 HOH B 55 455 62 HOH HOH . 
H 5 HOH B 56 456 90 HOH HOH . 
H 5 HOH B 57 457 75 HOH HOH . 
H 5 HOH B 58 458 106 HOH HOH . 
H 5 HOH B 59 459 116 HOH HOH . 
H 5 HOH B 60 460 181 HOH HOH . 
H 5 HOH B 61 461 84 HOH HOH . 
H 5 HOH B 62 462 130 HOH HOH . 
H 5 HOH B 63 463 95 HOH HOH . 
H 5 HOH B 64 464 138 HOH HOH . 
H 5 HOH B 65 465 137 HOH HOH . 
H 5 HOH B 66 466 173 HOH HOH . 
H 5 HOH B 67 467 86 HOH HOH . 
H 5 HOH B 68 468 168 HOH HOH . 
H 5 HOH B 69 469 125 HOH HOH . 
H 5 HOH B 70 470 105 HOH HOH . 
H 5 HOH B 71 471 160 HOH HOH . 
H 5 HOH B 72 472 180 HOH HOH . 
H 5 HOH B 73 473 93 HOH HOH . 
H 5 HOH B 74 474 132 HOH HOH . 
H 5 HOH B 75 475 65 HOH HOH . 
H 5 HOH B 76 476 119 HOH HOH . 
H 5 HOH B 77 477 100 HOH HOH . 
H 5 HOH B 78 478 124 HOH HOH . 
H 5 HOH B 79 479 83 HOH HOH . 
H 5 HOH B 80 480 28 HOH HOH . 
H 5 HOH B 81 481 99 HOH HOH . 
H 5 HOH B 82 482 174 HOH HOH . 
H 5 HOH B 83 483 64 HOH HOH . 
H 5 HOH B 84 484 169 HOH HOH . 
H 5 HOH B 85 485 126 HOH HOH . 
H 5 HOH B 86 486 121 HOH HOH . 
H 5 HOH B 87 487 79 HOH HOH . 
H 5 HOH B 88 488 67 HOH HOH . 
H 5 HOH B 89 489 164 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 N N1 UDP . . . C 2 12.687 14.194 21.848 1 35.58 ? N1 UDP 301 A 1 
HETATM 2 C C2 UDP . . . C 2 14.018 14.709 22.019 1 40.29 ? C2 UDP 301 A 1 
HETATM 3 N N3 UDP . . . C 2 14.179 16.03 22.185 1 39.64 ? N3 UDP 301 A 1 
HETATM 4 C C4 UDP . . . C 2 13.139 16.88 22.209 1 42.77 ? C4 UDP 301 A 1 
HETATM 5 C C5 UDP . . . C 2 11.848 16.41 22.037 1 38.1 ? C5 UDP 301 A 1 
HETATM 6 C C6 UDP . . . C 2 11.65 15.047 21.86 1 39.07 ? C6 UDP 301 A 1 
HETATM 7 O O2 UDP . . . C 2 15.063 14.006 22.011 1 36.38 ? O2 UDP 301 A 1 
HETATM 8 O O4 UDP . . . C 2 13.349 18.102 22.371 1 43.26 ? O4 UDP 301 A 1 
HETATM 9 C C1' UDP . . . C 2 12.419 12.769 21.675 1 36.76 ? C1' UDP 301 A 1 
HETATM 10 C C2' UDP . . . C 2 11.309 12.283 22.618 1 33.93 ? C2' UDP 301 A 1 
HETATM 11 O O2' UDP . . . C 2 11.858 11.994 23.895 1 30.72 ? O2' UDP 301 A 1 
HETATM 12 C C3' UDP . . . C 2 10.828 11.035 21.89 1 32.83 ? C3' UDP 301 A 1 
HETATM 13 C C4' UDP . . . C 2 11.057 11.335 20.418 1 37.57 ? C4' UDP 301 A 1 
HETATM 14 O O4' UDP . . . C 2 11.982 12.434 20.358 1 38 ? O4' UDP 301 A 1 
HETATM 15 O O3' UDP . . . C 2 11.626 9.922 22.255 1 29.04 ? O3' UDP 301 A 1 
HETATM 16 C C5' UDP . . . C 2 9.748 11.678 19.705 1 42.5 ? C5' UDP 301 A 1 
HETATM 17 O O5' UDP . . . C 2 9.23 12.855 20.323 1 50.32 ? O5' UDP 301 A 1 
HETATM 18 P PA UDP . . . C 2 7.709 13.375 20.109 1 56.15 ? PA UDP 301 A 1 
HETATM 19 O O1A UDP . . . C 2 6.901 12.229 19.568 1 66.73 ? O1A UDP 301 A 1 
HETATM 20 O O2A UDP . . . C 2 7.287 14.006 21.398 1 55.5 ? O2A UDP 301 A 1 
HETATM 21 O O3A UDP . . . C 2 7.869 14.502 18.961 1 75.71 ? O3A UDP 301 A 1 
HETATM 22 P PB UDP . . . C 2 8.826 15.808 19.117 1 93.88 ? PB UDP 301 A 1 
HETATM 23 O O1B UDP . . . C 2 8.415 16.693 17.958 1 92.55 ? O1B UDP 301 A 1 
HETATM 24 O O2B UDP . . . C 2 10.24 15.269 19.016 1 97.78 ? O2B UDP 301 A 1 
HETATM 25 O O3B UDP . . . C 2 8.498 16.392 20.477 1 94.66 ? O3B UDP 301 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#