data_6YWJ
#
_model_server_result.job_id            JhPAbARSy2K28xJuvJYFDw 
_model_server_result.datetime_utc      '2025-07-26 13:37:00' 
_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          6ywj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":402}' 
#
_entry.id    6YWJ 
#
_exptl.entry_id    6YWJ 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              324.181 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-MONOPHOSPHATE" 
_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         120 
_cell.entry_id            6YWJ 
_cell.length_a            104.343 
_cell.length_b            104.343 
_cell.length_c            127.845 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YWJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 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,D,G 1 1,2,3 
B,E,F,H 2 1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_775 -y+2,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 104.343 180.727377 0 
3 'crystal symmetry operation' 3_575 -x+y,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -104.343 180.727377 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F N N 
#
_chem_comp.formula           'C9 H13 N2 O9 P' 
_chem_comp.formula_weight    324.181 
_chem_comp.id                U5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_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 U5P sing 371 n n 
N1 C6 U5P sing 372 n n 
N1 C1' U5P sing 373 n n 
C2 N3 U5P sing 374 n n 
C2 O2 U5P doub 375 n n 
N3 C4 U5P sing 376 n n 
N3 HN3 U5P sing 377 n n 
C4 C5 U5P sing 378 n n 
C4 O4 U5P doub 379 n n 
C5 C6 U5P doub 380 n n 
C5 H5 U5P sing 381 n n 
C6 H6 U5P sing 382 n n 
C1' C2' U5P sing 383 n n 
C1' O4' U5P sing 384 n n 
C1' H1' U5P sing 385 n n 
C2' O2' U5P sing 386 n n 
C2' C3' U5P sing 387 n n 
C2' H2' U5P sing 388 n n 
O2' HO2' U5P sing 389 n n 
C3' C4' U5P sing 390 n n 
C3' O3' U5P sing 391 n n 
C3' H3' U5P sing 392 n n 
C4' O4' U5P sing 393 n n 
C4' C5' U5P sing 394 n n 
C4' H4' U5P sing 395 n n 
O3' HO3' U5P sing 396 n n 
C5' O5' U5P sing 397 n n 
C5' "H5'1" U5P sing 398 n n 
C5' "H5'2" U5P sing 399 n n 
O5' P U5P sing 400 n n 
P O1P U5P doub 401 n n 
P O2P U5P sing 402 n n 
P O3P U5P sing 403 n n 
O2P HOP2 U5P sing 404 n n 
O3P HOP3 U5P sing 405 n n 
#
_atom_sites.entry_id                     6YWJ 
_atom_sites.fract_transf_matrix[1][1]    0.009584 
_atom_sites.fract_transf_matrix[1][2]    0.005533 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011066 
_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]    0.007822 
_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 GOL A 1 401 401 GOL GOL . 
D 3 U5P A 1 402 1480 U5P U5P . 
E 2 GOL B 1 401 401 GOL GOL . 
F 3 U5P B 1 402 1481 U5P U5P . 
G 4 HOH A 1 501 6 HOH HOH . 
G 4 HOH A 2 502 2 HOH HOH . 
G 4 HOH A 3 503 4 HOH HOH . 
H 4 HOH B 1 501 7 HOH HOH . 
H 4 HOH B 2 502 1 HOH HOH . 
H 4 HOH B 3 503 8 HOH HOH . 
H 4 HOH B 4 504 5 HOH HOH . 
H 4 HOH B 5 505 3 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 U5P . . . F 3 10.674 100.225 26.139 1 33.63 ? N1 U5P 402 B 1 
HETATM 2 C C2 U5P . . . F 3 11.17 99.339 25.218 1 35.63 ? C2 U5P 402 B 1 
HETATM 3 N N3 U5P . . . F 3 10.236 98.573 24.602 1 39.4 ? N3 U5P 402 B 1 
HETATM 4 C C4 U5P . . . F 3 8.879 98.615 24.798 1 33.84 ? C4 U5P 402 B 1 
HETATM 5 C C5 U5P . . . F 3 8.438 99.585 25.74 1 38.32 ? C5 U5P 402 B 1 
HETATM 6 C C6 U5P . . . F 3 9.339 100.328 26.386 1 38.39 ? C6 U5P 402 B 1 
HETATM 7 O O2 U5P . . . F 3 12.361 99.233 24.985 1 38.22 ? O2 U5P 402 B 1 
HETATM 8 O O4 U5P . . . F 3 8.162 97.866 24.145 1 37.42 ? O4 U5P 402 B 1 
HETATM 9 C C1' U5P . . . F 3 11.673 101.053 26.835 1 35.35 ? C1' U5P 402 B 1 
HETATM 10 C C2' U5P . . . F 3 11.929 102.391 26.14 1 32.29 ? C2' U5P 402 B 1 
HETATM 11 O O2' U5P . . . F 3 13.32 102.583 26.29 1 41.26 ? O2' U5P 402 B 1 
HETATM 12 C C3' U5P . . . F 3 11.081 103.364 26.961 1 31.18 ? C3' U5P 402 B 1 
HETATM 13 C C4' U5P . . . F 3 11.08 102.721 28.353 1 35.99 ? C4' U5P 402 B 1 
HETATM 14 O O3' U5P . . . F 3 11.653 104.659 27.141 1 28.95 ? O3' U5P 402 B 1 
HETATM 15 O O4' U5P . . . F 3 11.224 101.294 28.15 1 33.53 ? O4' U5P 402 B 1 
HETATM 16 C C5' U5P . . . F 3 9.871 103.032 29.193 1 31.14 ? C5' U5P 402 B 1 
HETATM 17 O O5' U5P . . . F 3 10.2 104.153 30.055 1 32.79 ? O5' U5P 402 B 1 
HETATM 18 P P U5P . . . F 3 9.379 105.572 29.779 1 30.81 ? P U5P 402 B 1 
HETATM 19 O O1P U5P . . . F 3 9.81 105.937 28.324 1 29.49 ? O1P U5P 402 B 1 
HETATM 20 O O2P U5P . . . F 3 9.901 106.503 30.854 1 24.65 ? O2P U5P 402 B 1 
HETATM 21 O O3P U5P . . . F 3 7.932 105.282 29.91 1 25.87 ? O3P U5P 402 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           21 
#