data_8XFH
#
_model_server_result.job_id            de9w89NLjOtLp26iAiDgAA 
_model_server_result.datetime_utc      '2025-07-31 00:41:16' 
_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          8xfh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    8XFH 
#
_exptl.entry_id    8XFH 
_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            8XFH 
_cell.length_a            92.532 
_cell.length_b            103.354 
_cell.length_c            108.966 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XFH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    'P 2 2ab' 
_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 
_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 
#
_struct_conn.conn_type_id                   disulf 
_struct_conn.details                        ? 
_struct_conn.id                             disulf1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            SG 
_struct_conn.ptnr1_label_comp_id            CYS 
_struct_conn.ptnr1_label_seq_id             2 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             CYS 
_struct_conn.ptnr1_auth_seq_id              10 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            B 
_struct_conn.ptnr2_label_atom_id            SG 
_struct_conn.ptnr2_label_comp_id            CYS 
_struct_conn.ptnr2_label_seq_id             2 
_struct_conn.ptnr2_auth_asym_id             B 
_struct_conn.ptnr2_auth_comp_id             CYS 
_struct_conn.ptnr2_auth_seq_id              10 
_struct_conn.ptnr2_symmetry                 1_555 
_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                2.046 
_struct_conn.pdbx_value_order               ? 
#
_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 356 n n 
N1 C6 UDP sing 357 n n 
N1 C1' UDP sing 358 n n 
C2 N3 UDP sing 359 n n 
C2 O2 UDP doub 360 n n 
N3 C4 UDP sing 361 n n 
N3 HN3 UDP sing 362 n n 
C4 C5 UDP sing 363 n n 
C4 O4 UDP doub 364 n n 
C5 C6 UDP doub 365 n n 
C5 H5 UDP sing 366 n n 
C6 H6 UDP sing 367 n n 
C1' C2' UDP sing 368 n n 
C1' O4' UDP sing 369 n n 
C1' H1' UDP sing 370 n n 
C2' O2' UDP sing 371 n n 
C2' C3' UDP sing 372 n n 
C2' H2' UDP sing 373 n n 
O2' HO2' UDP sing 374 n n 
C3' C4' UDP sing 375 n n 
C3' O3' UDP sing 376 n n 
C3' H3' UDP sing 377 n n 
C4' O4' UDP sing 378 n n 
C4' C5' UDP sing 379 n n 
C4' H4' UDP sing 380 n n 
O3' HO3' UDP sing 381 n n 
C5' O5' UDP sing 382 n n 
C5' "H5'1" UDP sing 383 n n 
C5' "H5'2" UDP sing 384 n n 
O5' PA UDP sing 385 n n 
PA O1A UDP doub 386 n n 
PA O2A UDP sing 387 n n 
PA O3A UDP sing 388 n n 
O2A HOA2 UDP sing 389 n n 
O3A PB UDP sing 390 n n 
PB O1B UDP doub 391 n n 
PB O2B UDP sing 392 n n 
PB O3B UDP sing 393 n n 
O2B HOB2 UDP sing 394 n n 
O3B HOB3 UDP sing 395 n n 
#
_atom_sites.entry_id                     8XFH 
_atom_sites.fract_transf_matrix[1][1]    0.010807 
_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]    0.009675 
_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]    0.009177 
_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 1 501 1 UDP UDP . 
D 2 UDP B 1 501 2 UDP UDP . 
#
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 2 113.192 16.875 47.437 1 28.76 ? N1 UDP 501 A 1 
HETATM 2 C C2 UDP . . . C 2 114.419 16.503 46.924 1 30.55 ? C2 UDP 501 A 1 
HETATM 3 N N3 UDP . . . C 2 115.441 16.112 47.769 1 31.62 ? N3 UDP 501 A 1 
HETATM 4 C C4 UDP . . . C 2 115.241 16.094 49.135 1 29.61 ? C4 UDP 501 A 1 
HETATM 5 C C5 UDP . . . C 2 114.005 16.473 49.645 1 28.81 ? C5 UDP 501 A 1 
HETATM 6 C C6 UDP . . . C 2 113.023 16.961 48.79 1 29.15 ? C6 UDP 501 A 1 
HETATM 7 O O2 UDP . . . C 2 114.6 16.52 45.706 1 32.24 ? O2 UDP 501 A 1 
HETATM 8 O O4 UDP . . . C 2 116.146 15.747 49.895 1 32.31 ? O4 UDP 501 A 1 
HETATM 9 C C1' UDP . . . C 2 112.118 17.306 46.516 1 33.85 ? C1' UDP 501 A 1 
HETATM 10 C C2' UDP . . . C 2 111.269 16.141 46.028 1 32.05 ? C2' UDP 501 A 1 
HETATM 11 O O2' UDP . . . C 2 111.665 15.727 44.741 1 31.35 ? O2' UDP 501 A 1 
HETATM 12 C C3' UDP . . . C 2 109.856 16.679 45.99 1 28.04 ? C3' UDP 501 A 1 
HETATM 13 C C4' UDP . . . C 2 109.908 17.998 46.742 1 26.97 ? C4' UDP 501 A 1 
HETATM 14 O O4' UDP . . . C 2 111.242 18.214 47.159 1 29.2 ? O4' UDP 501 A 1 
HETATM 15 O O3' UDP . . . C 2 109.481 16.917 44.655 1 32.87 ? O3' UDP 501 A 1 
HETATM 16 C C5' UDP . . . C 2 108.982 17.971 47.949 1 30.11 ? C5' UDP 501 A 1 
HETATM 17 O O5' UDP . . . C 2 107.663 17.755 47.503 1 32.44 ? O5' UDP 501 A 1 
HETATM 18 P PA UDP . . . C 2 106.51 17.331 48.534 1 28.24 ? PA UDP 501 A 1 
HETATM 19 O O1A UDP . . . C 2 105.239 17.062 47.829 1 32.68 ? O1A UDP 501 A 1 
HETATM 20 O O2A UDP . . . C 2 106.957 16.152 49.303 1 24.64 ? O2A UDP 501 A 1 
HETATM 21 O O3A UDP . . . C 2 106.348 18.613 49.491 1 33.84 ? O3A UDP 501 A 1 
HETATM 22 P PB UDP . . . C 2 106.873 18.625 51.011 1 30.52 ? PB UDP 501 A 1 
HETATM 23 O O1B UDP . . . C 2 108.348 18.567 51.011 1 31.27 ? O1B UDP 501 A 1 
HETATM 24 O O2B UDP . . . C 2 106.371 17.445 51.742 1 27.68 ? O2B UDP 501 A 1 
HETATM 25 O O3B UDP . . . C 2 106.394 19.863 51.657 1 36.98 ? O3B UDP 501 A 1 
#
_model_server_stats.io_time_ms              59 
_model_server_stats.parse_time_ms           44 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           1015 
_model_server_stats.encode_time_ms          20 
_model_server_stats.element_count           25 
#