data_6YWJ
#
_model_server_result.job_id            f3ZMRDWFpCwMqgYtYYbWHg 
_model_server_result.datetime_utc      '2024-12-22 03:01:15' 
_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":"D","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 . . . D 3 19.681 108.97 2.96 1 36.06 ? N1 U5P 402 A 1 
HETATM 2 C C2 U5P . . . D 3 20.569 108.403 3.846 1 39.08 ? C2 U5P 402 A 1 
HETATM 3 N N3 U5P . . . D 3 21.417 109.282 4.469 1 34.95 ? N3 U5P 402 A 1 
HETATM 4 C C4 U5P . . . D 3 21.504 110.638 4.25 1 36.27 ? C4 U5P 402 A 1 
HETATM 5 C C5 U5P . . . D 3 20.526 111.152 3.343 1 35.29 ? C5 U5P 402 A 1 
HETATM 6 C C6 U5P . . . D 3 19.69 110.314 2.714 1 35.94 ? C6 U5P 402 A 1 
HETATM 7 O O2 U5P . . . D 3 20.595 107.2 4.043 1 35.48 ? O2 U5P 402 A 1 
HETATM 8 O O4 U5P . . . D 3 22.328 111.315 4.877 1 41.09 ? O4 U5P 402 A 1 
HETATM 9 C C1' U5P . . . D 3 18.791 108.052 2.242 1 36.02 ? C1' U5P 402 A 1 
HETATM 10 C C2' U5P . . . D 3 17.422 107.855 2.891 1 36.29 ? C2' U5P 402 A 1 
HETATM 11 O O2' U5P . . . D 3 17.324 106.448 2.777 1 42.02 ? O2' U5P 402 A 1 
HETATM 12 C C3' U5P . . . D 3 16.462 108.64 1.968 1 36.88 ? C3' U5P 402 A 1 
HETATM 13 C C4' U5P . . . D 3 17.184 108.577 0.617 1 35.74 ? C4' U5P 402 A 1 
HETATM 14 O O3' U5P . . . D 3 15.175 108.054 1.798 1 37.52 ? O3' U5P 402 A 1 
HETATM 15 O O4' U5P . . . D 3 18.593 108.587 0.956 1 37.96 ? O4' U5P 402 A 1 
HETATM 16 C C5' U5P . . . D 3 16.918 109.7 -0.351 1 32.35 ? C5' U5P 402 A 1 
HETATM 17 O O5' U5P . . . D 3 15.695 109.454 -1.08 1 28.6 ? O5' U5P 402 A 1 
HETATM 18 P P U5P . . . D 3 14.444 110.415 -0.716 1 31.95 ? P U5P 402 A 1 
HETATM 19 O O1P U5P . . . D 3 13.394 109.862 -1.68 1 25.46 ? O1P U5P 402 A 1 
HETATM 20 O O2P U5P . . . D 3 14.145 110.287 0.771 1 22.56 ? O2P U5P 402 A 1 
HETATM 21 O O3P U5P . . . D 3 14.855 111.853 -1.022 1 28.48 ? O3P U5P 402 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           316 
_model_server_stats.encode_time_ms          16 
_model_server_stats.element_count           21 
#