data_8W53
#
_model_server_result.job_id            lH7iQVw4bFA8zJBldyJUZg 
_model_server_result.datetime_utc      '2024-10-11 04:31:37' 
_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          8w53 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    8W53 
#
_exptl.entry_id    8W53 
_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            8W53 
_cell.length_a            72.442 
_cell.length_b            80.841 
_cell.length_c            180.242 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8W53 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    'P 2 2ab (z,x,y)' 
_symmetry.space_group_name_H-M     'P 2 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,F 1 1 
B,D,E,G 2 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 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                     8W53 
_atom_sites.fract_transf_matrix[1][1]    0.013804 
_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]    0.01237 
_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]    0.005548 
_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 B 1 501 1 UDP UDP . 
D 2 UDP A 1 501 2 UDP UDP . 
E 3 GOL A 1 502 1 GOL GOL . 
F 4 HOH B 1 601 29 HOH HOH . 
F 4 HOH B 2 602 49 HOH HOH . 
F 4 HOH B 3 603 48 HOH HOH . 
F 4 HOH B 4 604 52 HOH HOH . 
F 4 HOH B 5 605 54 HOH HOH . 
F 4 HOH B 6 606 31 HOH HOH . 
F 4 HOH B 7 607 10 HOH HOH . 
F 4 HOH B 8 608 46 HOH HOH . 
F 4 HOH B 9 609 17 HOH HOH . 
F 4 HOH B 10 610 53 HOH HOH . 
F 4 HOH B 11 611 9 HOH HOH . 
F 4 HOH B 12 612 36 HOH HOH . 
F 4 HOH B 13 613 50 HOH HOH . 
F 4 HOH B 14 614 8 HOH HOH . 
F 4 HOH B 15 615 37 HOH HOH . 
F 4 HOH B 16 616 41 HOH HOH . 
F 4 HOH B 17 617 6 HOH HOH . 
F 4 HOH B 18 618 24 HOH HOH . 
F 4 HOH B 19 619 27 HOH HOH . 
F 4 HOH B 20 620 28 HOH HOH . 
F 4 HOH B 21 621 18 HOH HOH . 
F 4 HOH B 22 622 21 HOH HOH . 
F 4 HOH B 23 623 47 HOH HOH . 
F 4 HOH B 24 624 32 HOH HOH . 
F 4 HOH B 25 625 11 HOH HOH . 
F 4 HOH B 26 626 30 HOH HOH . 
F 4 HOH B 27 627 42 HOH HOH . 
G 4 HOH A 1 601 4 HOH HOH . 
G 4 HOH A 2 602 38 HOH HOH . 
G 4 HOH A 3 603 20 HOH HOH . 
G 4 HOH A 4 604 26 HOH HOH . 
G 4 HOH A 5 605 2 HOH HOH . 
G 4 HOH A 6 606 12 HOH HOH . 
G 4 HOH A 7 607 5 HOH HOH . 
G 4 HOH A 8 608 7 HOH HOH . 
G 4 HOH A 9 609 22 HOH HOH . 
G 4 HOH A 10 610 51 HOH HOH . 
G 4 HOH A 11 611 39 HOH HOH . 
G 4 HOH A 12 612 13 HOH HOH . 
G 4 HOH A 13 613 23 HOH HOH . 
G 4 HOH A 14 614 16 HOH HOH . 
G 4 HOH A 15 615 25 HOH HOH . 
G 4 HOH A 16 616 35 HOH HOH . 
G 4 HOH A 17 617 34 HOH HOH . 
G 4 HOH A 18 618 1 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 . . . D 2 -38.92 -57.813 32.539 1 69.74 ? N1 UDP 501 A 1 
HETATM 2 C C2 UDP . . . D 2 -39.223 -58.576 33.65 1 71.32 ? C2 UDP 501 A 1 
HETATM 3 N N3 UDP . . . D 2 -40.092 -57.991 34.538 1 69.5 ? N3 UDP 501 A 1 
HETATM 4 C C4 UDP . . . D 2 -40.676 -56.744 34.425 1 70.45 ? C4 UDP 501 A 1 
HETATM 5 C C5 UDP . . . D 2 -40.314 -56.017 33.247 1 64.02 ? C5 UDP 501 A 1 
HETATM 6 C C6 UDP . . . D 2 -39.464 -56.561 32.359 1 67.78 ? C6 UDP 501 A 1 
HETATM 7 O O2 UDP . . . D 2 -38.755 -59.69 33.839 1 72.01 ? O2 UDP 501 A 1 
HETATM 8 O O4 UDP . . . D 2 -41.447 -56.347 35.313 1 68.33 ? O4 UDP 501 A 1 
HETATM 9 C C1' UDP . . . D 2 -37.989 -58.384 31.553 1 62.02 ? C1' UDP 501 A 1 
HETATM 10 C C2' UDP . . . D 2 -38.678 -58.902 30.287 1 60.52 ? C2' UDP 501 A 1 
HETATM 11 O O2' UDP . . . D 2 -38.941 -60.296 30.402 1 67.32 ? O2' UDP 501 A 1 
HETATM 12 C C3' UDP . . . D 2 -37.623 -58.607 29.221 1 56.35 ? C3' UDP 501 A 1 
HETATM 13 C C4' UDP . . . D 2 -37.036 -57.289 29.708 1 63.31 ? C4' UDP 501 A 1 
HETATM 14 O O4' UDP . . . D 2 -37.086 -57.367 31.149 1 66.44 ? O4' UDP 501 A 1 
HETATM 15 O O3' UDP . . . D 2 -36.625 -59.62 29.159 1 59.85 ? O3' UDP 501 A 1 
HETATM 16 C C5' UDP . . . D 2 -37.774 -56.057 29.249 1 61.45 ? C5' UDP 501 A 1 
HETATM 17 O O5' UDP . . . D 2 -37.055 -55.438 28.162 1 58.77 ? O5' UDP 501 A 1 
HETATM 18 P PA UDP . . . D 2 -37.809 -54.927 26.87 1 56.99 ? PA UDP 501 A 1 
HETATM 19 O O1A UDP . . . D 2 -36.922 -55.197 25.714 1 61.72 ? O1A UDP 501 A 1 
HETATM 20 O O2A UDP . . . D 2 -39.219 -55.503 26.792 1 57.19 ? O2A UDP 501 A 1 
HETATM 21 O O3A UDP . . . D 2 -37.98 -53.345 27.083 1 56.66 ? O3A UDP 501 A 1 
HETATM 22 P PB UDP . . . D 2 -37.325 -52.381 28.159 1 59.53 ? PB UDP 501 A 1 
HETATM 23 O O1B UDP . . . D 2 -36.171 -51.734 27.391 1 69.75 ? O1B UDP 501 A 1 
HETATM 24 O O2B UDP . . . D 2 -38.41 -51.333 28.387 1 68.95 ? O2B UDP 501 A 1 
HETATM 25 O O3B UDP . . . D 2 -36.912 -53.101 29.398 1 65.02 ? O3B UDP 501 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#