data_7W0K
#
_model_server_result.job_id            9d3EVYzvm6QAjbT7dKhUSA 
_model_server_result.datetime_utc      '2024-11-05 21:03:34' 
_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          7w0k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":501}' 
#
_entry.id    7W0K 
#
_exptl.entry_id    7W0K 
_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    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          114.4 
_cell.angle_gamma         90 
_cell.entry_id            7W0K 
_cell.length_a            54.462 
_cell.length_b            74.038 
_cell.length_c            61.815 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7W0K 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
#
_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 
#
_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 371 n n 
N1 C6 UDP sing 372 n n 
N1 C1' UDP sing 373 n n 
C2 N3 UDP sing 374 n n 
C2 O2 UDP doub 375 n n 
N3 C4 UDP sing 376 n n 
N3 HN3 UDP sing 377 n n 
C4 C5 UDP sing 378 n n 
C4 O4 UDP doub 379 n n 
C5 C6 UDP doub 380 n n 
C5 H5 UDP sing 381 n n 
C6 H6 UDP sing 382 n n 
C1' C2' UDP sing 383 n n 
C1' O4' UDP sing 384 n n 
C1' H1' UDP sing 385 n n 
C2' O2' UDP sing 386 n n 
C2' C3' UDP sing 387 n n 
C2' H2' UDP sing 388 n n 
O2' HO2' UDP sing 389 n n 
C3' C4' UDP sing 390 n n 
C3' O3' UDP sing 391 n n 
C3' H3' UDP sing 392 n n 
C4' O4' UDP sing 393 n n 
C4' C5' UDP sing 394 n n 
C4' H4' UDP sing 395 n n 
O3' HO3' UDP sing 396 n n 
C5' O5' UDP sing 397 n n 
C5' "H5'1" UDP sing 398 n n 
C5' "H5'2" UDP sing 399 n n 
O5' PA UDP sing 400 n n 
PA O1A UDP doub 401 n n 
PA O2A UDP sing 402 n n 
PA O3A UDP sing 403 n n 
O2A HOA2 UDP sing 404 n n 
O3A PB UDP sing 405 n n 
PB O1B UDP doub 406 n n 
PB O2B UDP sing 407 n n 
PB O3B UDP sing 408 n n 
O2B HOB2 UDP sing 409 n n 
O3B HOB3 UDP sing 410 n n 
#
_atom_sites.entry_id                     7W0K 
_atom_sites.fract_transf_matrix[1][1]    0.018361 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.008329 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013507 
_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]    0.017764 
_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 UDP A 1 501 504 UDP UDP . 
C 3 GOL A 1 502 505 GOL LIG . 
D 3 GOL A 1 503 506 GOL LIG . 
E 3 GOL A 1 504 507 GOL LIG . 
F 4 HOH A 1 601 1 HOH HOH . 
F 4 HOH A 2 602 6 HOH HOH . 
F 4 HOH A 3 603 2 HOH HOH . 
F 4 HOH A 4 604 17 HOH HOH . 
F 4 HOH A 5 605 29 HOH HOH . 
F 4 HOH A 6 606 25 HOH HOH . 
F 4 HOH A 7 607 60 HOH HOH . 
F 4 HOH A 8 608 5 HOH HOH . 
F 4 HOH A 9 609 4 HOH HOH . 
F 4 HOH A 10 610 14 HOH HOH . 
F 4 HOH A 11 611 27 HOH HOH . 
F 4 HOH A 12 612 21 HOH HOH . 
F 4 HOH A 13 613 3 HOH HOH . 
F 4 HOH A 14 614 12 HOH HOH . 
F 4 HOH A 15 615 20 HOH HOH . 
F 4 HOH A 16 616 19 HOH HOH . 
F 4 HOH A 17 617 11 HOH HOH . 
F 4 HOH A 18 618 28 HOH HOH . 
F 4 HOH A 19 619 88 HOH HOH . 
F 4 HOH A 20 620 104 HOH HOH . 
F 4 HOH A 21 621 7 HOH HOH . 
F 4 HOH A 22 622 76 HOH HOH . 
F 4 HOH A 23 623 70 HOH HOH . 
F 4 HOH A 24 624 102 HOH HOH . 
F 4 HOH A 25 625 23 HOH HOH . 
F 4 HOH A 26 626 15 HOH HOH . 
F 4 HOH A 27 627 8 HOH HOH . 
F 4 HOH A 28 628 71 HOH HOH . 
F 4 HOH A 29 629 105 HOH HOH . 
F 4 HOH A 30 630 24 HOH HOH . 
F 4 HOH A 31 631 131 HOH HOH . 
F 4 HOH A 32 632 61 HOH HOH . 
F 4 HOH A 33 633 245 HOH HOH . 
F 4 HOH A 34 634 153 HOH HOH . 
F 4 HOH A 35 635 151 HOH HOH . 
F 4 HOH A 36 636 226 HOH HOH . 
F 4 HOH A 37 637 182 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 . . . B 2 -5.533 -0.795 -8.687 1 22.64 ? N1 UDP 501 A 1 
HETATM 2 C C2 UDP . . . B 2 -4.461 -1.48 -8.33 1 20.1 ? C2 UDP 501 A 1 
HETATM 3 N N3 UDP . . . B 2 -3.982 -2.442 -9.089 1 23.59 ? N3 UDP 501 A 1 
HETATM 4 C C4 UDP . . . B 2 -4.551 -2.73 -10.252 1 20.62 ? C4 UDP 501 A 1 
HETATM 5 C C5 UDP . . . B 2 -5.679 -2.035 -10.674 1 20.73 ? C5 UDP 501 A 1 
HETATM 6 C C6 UDP . . . B 2 -6.162 -1.039 -9.834 1 22.35 ? C6 UDP 501 A 1 
HETATM 7 O O2 UDP . . . B 2 -3.81 -1.2 -7.133 1 23.07 ? O2 UDP 501 A 1 
HETATM 8 O O4 UDP . . . B 2 -4.016 -3.759 -11.023 1 20.36 ? O4 UDP 501 A 1 
HETATM 9 C C1' UDP . . . B 2 -6.049 0.257 -7.8 1 23.32 ? C1' UDP 501 A 1 
HETATM 10 C C2' UDP . . . B 2 -5.947 1.625 -8.471 1 20.23 ? C2' UDP 501 A 1 
HETATM 11 O O2' UDP . . . B 2 -4.679 2.077 -8.277 1 17.34 ? O2' UDP 501 A 1 
HETATM 12 C C3' UDP . . . B 2 -7.071 2.408 -7.741 1 21.77 ? C3' UDP 501 A 1 
HETATM 13 C C4' UDP . . . B 2 -8.015 1.515 -7.513 1 19.97 ? C4' UDP 501 A 1 
HETATM 14 O O4' UDP . . . B 2 -7.327 0.08 -7.635 1 23.49 ? O4' UDP 501 A 1 
HETATM 15 O O3' UDP . . . B 2 -6.627 3.002 -6.439 1 21.08 ? O3' UDP 501 A 1 
HETATM 16 C C5' UDP . . . B 2 -9.112 1.583 -8.566 1 19.58 ? C5' UDP 501 A 1 
HETATM 17 O O5' UDP . . . B 2 -9.938 2.636 -8.173 1 21.21 ? O5' UDP 501 A 1 
HETATM 18 P PA UDP . . . B 2 -10.718 3.529 -9.293 1 17.86 ? PA UDP 501 A 1 
HETATM 19 O O1A UDP . . . B 2 -9.804 3.907 -10.438 1 19.69 -1 O1A UDP 501 A 1 
HETATM 20 O O2A UDP . . . B 2 -11.257 4.751 -8.612 1 20.88 ? O2A UDP 501 A 1 
HETATM 21 O O3A UDP . . . B 2 -11.915 2.682 -10.015 1 21.59 ? O3A UDP 501 A 1 
HETATM 22 P PB UDP . . . B 2 -12.87 1.514 -9.393 1 21.71 ? PB UDP 501 A 1 
HETATM 23 O O1B UDP . . . B 2 -13.905 1.301 -10.474 1 23.15 -1 O1B UDP 501 A 1 
HETATM 24 O O2B UDP . . . B 2 -12.056 0.282 -9.131 1 23.44 ? O2B UDP 501 A 1 
HETATM 25 O O3B UDP . . . B 2 -13.526 2.032 -8.131 1 21.27 ? O3B UDP 501 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#