data_7W0Z
#
_model_server_result.job_id            16sriy-Dmdklo2YxVT6Uhg 
_model_server_result.datetime_utc      '2024-11-24 17:30:06' 
_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          7w0z 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":501}' 
#
_entry.id    7W0Z 
#
_exptl.entry_id    7W0Z 
_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          96.92 
_cell.angle_gamma         90 
_cell.entry_id            7W0Z 
_cell.length_a            51.026 
_cell.length_b            76.553 
_cell.length_c            63.553 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7W0Z 
_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 
_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 423 n n 
N1 C6 UDP sing 424 n n 
N1 C1' UDP sing 425 n n 
C2 N3 UDP sing 426 n n 
C2 O2 UDP doub 427 n n 
N3 C4 UDP sing 428 n n 
N3 HN3 UDP sing 429 n n 
C4 C5 UDP sing 430 n n 
C4 O4 UDP doub 431 n n 
C5 C6 UDP doub 432 n n 
C5 H5 UDP sing 433 n n 
C6 H6 UDP sing 434 n n 
C1' C2' UDP sing 435 n n 
C1' O4' UDP sing 436 n n 
C1' H1' UDP sing 437 n n 
C2' O2' UDP sing 438 n n 
C2' C3' UDP sing 439 n n 
C2' H2' UDP sing 440 n n 
O2' HO2' UDP sing 441 n n 
C3' C4' UDP sing 442 n n 
C3' O3' UDP sing 443 n n 
C3' H3' UDP sing 444 n n 
C4' O4' UDP sing 445 n n 
C4' C5' UDP sing 446 n n 
C4' H4' UDP sing 447 n n 
O3' HO3' UDP sing 448 n n 
C5' O5' UDP sing 449 n n 
C5' "H5'1" UDP sing 450 n n 
C5' "H5'2" UDP sing 451 n n 
O5' PA UDP sing 452 n n 
PA O1A UDP doub 453 n n 
PA O2A UDP sing 454 n n 
PA O3A UDP sing 455 n n 
O2A HOA2 UDP sing 456 n n 
O3A PB UDP sing 457 n n 
PB O1B UDP doub 458 n n 
PB O2B UDP sing 459 n n 
PB O3B UDP sing 460 n n 
O2B HOB2 UDP sing 461 n n 
O3B HOB3 UDP sing 462 n n 
#
_atom_sites.entry_id                     7W0Z 
_atom_sites.fract_transf_matrix[1][1]    0.019598 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00238 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013063 
_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]    0.01585 
_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 1 501 501 UDP UDP . 
C 3 6JI A 1 502 502 6JI RES . 
D 4 HOH A 1 601 43 HOH HOH . 
D 4 HOH A 2 602 22 HOH HOH . 
D 4 HOH A 3 603 17 HOH HOH . 
D 4 HOH A 4 604 37 HOH HOH . 
D 4 HOH A 5 605 23 HOH HOH . 
D 4 HOH A 6 606 40 HOH HOH . 
D 4 HOH A 7 607 2 HOH HOH . 
D 4 HOH A 8 608 11 HOH HOH . 
D 4 HOH A 9 609 25 HOH HOH . 
D 4 HOH A 10 610 3 HOH HOH . 
D 4 HOH A 11 611 5 HOH HOH . 
D 4 HOH A 12 612 1 HOH HOH . 
D 4 HOH A 13 613 6 HOH HOH . 
D 4 HOH A 14 614 4 HOH HOH . 
D 4 HOH A 15 615 21 HOH HOH . 
D 4 HOH A 16 616 18 HOH HOH . 
D 4 HOH A 17 617 13 HOH HOH . 
D 4 HOH A 18 618 33 HOH HOH . 
D 4 HOH A 19 619 77 HOH HOH . 
D 4 HOH A 20 620 71 HOH HOH . 
D 4 HOH A 21 621 24 HOH HOH . 
D 4 HOH A 22 622 20 HOH HOH . 
D 4 HOH A 23 623 85 HOH HOH . 
D 4 HOH A 24 624 8 HOH HOH . 
D 4 HOH A 25 625 42 HOH HOH . 
D 4 HOH A 26 626 35 HOH HOH . 
D 4 HOH A 27 627 19 HOH HOH . 
D 4 HOH A 28 628 98 HOH HOH . 
D 4 HOH A 29 629 10 HOH HOH . 
D 4 HOH A 30 630 16 HOH HOH . 
D 4 HOH A 31 631 36 HOH HOH . 
D 4 HOH A 32 632 293 HOH HOH . 
D 4 HOH A 33 633 12 HOH HOH . 
D 4 HOH A 34 634 7 HOH HOH . 
D 4 HOH A 35 635 14 HOH HOH . 
D 4 HOH A 36 636 28 HOH HOH . 
D 4 HOH A 37 637 272 HOH HOH . 
D 4 HOH A 38 638 30 HOH HOH . 
D 4 HOH A 39 639 26 HOH HOH . 
D 4 HOH A 40 640 39 HOH HOH . 
D 4 HOH A 41 641 53 HOH HOH . 
D 4 HOH A 42 642 27 HOH HOH . 
D 4 HOH A 43 643 45 HOH HOH . 
D 4 HOH A 44 644 38 HOH HOH . 
D 4 HOH A 45 645 99 HOH HOH . 
D 4 HOH A 46 646 34 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 44.486 35.476 41.835 1 17.65 ? N1 UDP 501 A 1 
HETATM 2 C C2 UDP . . . B 2 45.385 36.161 41.167 1 17.64 ? C2 UDP 501 A 1 
HETATM 3 N N3 UDP . . . B 2 46.058 37.14 41.71 1 17.3 ? N3 UDP 501 A 1 
HETATM 4 C C4 UDP . . . B 2 45.843 37.454 42.966 1 16.99 ? C4 UDP 501 A 1 
HETATM 5 C C5 UDP . . . B 2 44.898 36.774 43.735 1 17.68 ? C5 UDP 501 A 1 
HETATM 6 C C6 UDP . . . B 2 44.202 35.745 43.106 1 17.23 ? C6 UDP 501 A 1 
HETATM 7 O O2 UDP . . . B 2 45.639 35.834 39.841 1 14.45 ? O2 UDP 501 A 1 
HETATM 8 O O4 UDP . . . B 2 46.584 38.502 43.492 1 18.16 ? O4 UDP 501 A 1 
HETATM 9 C C1' UDP . . . B 2 43.779 34.412 41.1 1 17.92 ? C1' UDP 501 A 1 
HETATM 10 C C2' UDP . . . B 2 44.198 33.011 41.58 1 18.85 ? C2' UDP 501 A 1 
HETATM 11 O O2' UDP . . . B 2 45.249 32.563 40.818 1 16.3 ? O2' UDP 501 A 1 
HETATM 12 C C3' UDP . . . B 2 42.905 32.19 41.369 1 15.93 ? C3' UDP 501 A 1 
HETATM 13 C C4' UDP . . . B 2 41.911 33.045 41.551 1 16.59 ? C4' UDP 501 A 1 
HETATM 14 O O4' UDP . . . B 2 42.481 34.53 41.305 1 17.59 ? O4' UDP 501 A 1 
HETATM 15 O O3' UDP . . . B 2 42.89 31.692 39.952 1 19.61 ? O3' UDP 501 A 1 
HETATM 16 C C5' UDP . . . B 2 41.327 32.983 42.954 1 16.55 ? C5' UDP 501 A 1 
HETATM 17 O O5' UDP . . . B 2 40.304 32.021 42.925 1 14.38 ? O5' UDP 501 A 1 
HETATM 18 P PA UDP . . . B 2 40.058 31.09 44.243 1 15.16 ? PA UDP 501 A 1 
HETATM 19 O O1A UDP . . . B 2 39.315 29.822 43.871 1 15.29 ? O1A UDP 501 A 1 
HETATM 20 O O2A UDP . . . B 2 41.351 30.743 44.932 1 16.32 -1 O2A UDP 501 A 1 
HETATM 21 O O3A UDP . . . B 2 39.227 31.981 45.328 1 18.21 ? O3A UDP 501 A 1 
HETATM 22 P PB UDP . . . B 2 38.025 33.067 45.026 1 17.81 ? PB UDP 501 A 1 
HETATM 23 O O1B UDP . . . B 2 37.093 32.494 43.983 1 16.84 ? O1B UDP 501 A 1 
HETATM 24 O O2B UDP . . . B 2 38.598 34.395 44.612 1 17.06 -1 O2B UDP 501 A 1 
HETATM 25 O O3B UDP . . . B 2 37.374 33.198 46.391 1 19.04 ? O3B UDP 501 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           225 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#