data_1XTV
#
_model_server_result.job_id            YKBnCYte29TWLC_6Hx6LKQ 
_model_server_result.datetime_utc      '2024-10-14 04:23:49' 
_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          1xtv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":3250}' 
#
_entry.id    1XTV 
#
_exptl.entry_id    1XTV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              324.181 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         85.82 
_cell.angle_beta          85.28 
_cell.angle_gamma         62.46 
_cell.entry_id            1XTV 
_cell.length_a            68.1 
_cell.length_b            73.57 
_cell.length_c            115.1 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1XTV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 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,B,C,D,I,J 1 1 
E,F,G,H,K,L 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 I N N 
? 2 J N N 
? 2 K N N 
? 2 L 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 315 n n 
N1 C6 U5P sing 316 n n 
N1 C1' U5P sing 317 n n 
C2 N3 U5P sing 318 n n 
C2 O2 U5P doub 319 n n 
N3 C4 U5P sing 320 n n 
N3 HN3 U5P sing 321 n n 
C4 C5 U5P sing 322 n n 
C4 O4 U5P doub 323 n n 
C5 C6 U5P doub 324 n n 
C5 H5 U5P sing 325 n n 
C6 H6 U5P sing 326 n n 
C1' C2' U5P sing 327 n n 
C1' O4' U5P sing 328 n n 
C1' H1' U5P sing 329 n n 
C2' O2' U5P sing 330 n n 
C2' C3' U5P sing 331 n n 
C2' H2' U5P sing 332 n n 
O2' HO2' U5P sing 333 n n 
C3' C4' U5P sing 334 n n 
C3' O3' U5P sing 335 n n 
C3' H3' U5P sing 336 n n 
C4' O4' U5P sing 337 n n 
C4' C5' U5P sing 338 n n 
C4' H4' U5P sing 339 n n 
O3' HO3' U5P sing 340 n n 
C5' O5' U5P sing 341 n n 
C5' "H5'1" U5P sing 342 n n 
C5' "H5'2" U5P sing 343 n n 
O5' P U5P sing 344 n n 
P O1P U5P doub 345 n n 
P O2P U5P sing 346 n n 
P O3P U5P sing 347 n n 
O2P HOP2 U5P sing 348 n n 
O3P HOP3 U5P sing 349 n n 
#
_atom_sites.entry_id                     1XTV 
_atom_sites.fract_transf_matrix[1][1]    0.014684 
_atom_sites.fract_transf_matrix[1][2]    -0.007657 
_atom_sites.fract_transf_matrix[1][3]    -0.000911 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01533 
_atom_sites.fract_transf_matrix[2][3]    -0.000605 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.008724 
_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
I 2 U5P A 1 1250 250 U5P UMP . 
J 2 U5P C 1 2250 250 U5P UMP . 
K 2 U5P E 1 3250 250 U5P UMP . 
L 2 U5P G 1 4250 250 U5P UMP . 
#
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 . . . K 2 74.422 9.117 37.111 1 22.89 ? N1 U5P 3250 E 1 
HETATM 2 C C2 U5P . . . K 2 75.507 9.578 37.945 1 24.63 ? C2 U5P 3250 E 1 
HETATM 3 N N3 U5P . . . K 2 76.821 9.364 37.448 1 25.04 ? N3 U5P 3250 E 1 
HETATM 4 C C4 U5P . . . K 2 77.064 8.72 36.215 1 19.07 ? C4 U5P 3250 E 1 
HETATM 5 C C5 U5P . . . K 2 75.963 8.235 35.423 1 12.64 ? C5 U5P 3250 E 1 
HETATM 6 C C6 U5P . . . K 2 74.578 8.461 35.914 1 19.37 ? C6 U5P 3250 E 1 
HETATM 7 O O2 U5P . . . K 2 75.31 10.185 39.117 1 32.87 ? O2 U5P 3250 E 1 
HETATM 8 O O4 U5P . . . K 2 78.222 8.584 35.837 1 28.74 ? O4 U5P 3250 E 1 
HETATM 9 C C1' U5P . . . K 2 72.977 9.356 37.619 1 31.22 ? C1' U5P 3250 E 1 
HETATM 10 C C2' U5P . . . K 2 72.558 10.827 37.957 1 35.8 ? C2' U5P 3250 E 1 
HETATM 11 O O2' U5P . . . K 2 72.354 10.921 39.336 1 41.95 ? O2' U5P 3250 E 1 
HETATM 12 C C3' U5P . . . K 2 71.293 11.108 37.044 1 35.51 ? C3' U5P 3250 E 1 
HETATM 13 C C4' U5P . . . K 2 71.076 9.836 36.277 1 37.3 ? C4' U5P 3250 E 1 
HETATM 14 O O3' U5P . . . K 2 70.174 11.4 37.965 1 34.21 ? O3' U5P 3250 E 1 
HETATM 15 O O4' U5P . . . K 2 72.074 8.824 36.636 1 29.52 ? O4' U5P 3250 E 1 
HETATM 16 C C5' U5P . . . K 2 71.19 9.858 34.797 1 34.31 ? C5' U5P 3250 E 1 
HETATM 17 O O5' U5P . . . K 2 71.585 8.707 34.125 1 36.95 ? O5' U5P 3250 E 1 
HETATM 18 P P U5P . . . K 2 70.874 8.299 32.772 1 31.81 ? P U5P 3250 E 1 
HETATM 19 O O1P U5P . . . K 2 69.396 8.18 33.105 1 26.05 ? O1P U5P 3250 E 1 
HETATM 20 O O2P U5P . . . K 2 71.196 9.408 31.778 1 31.06 ? O2P U5P 3250 E 1 
HETATM 21 O O3P U5P . . . K 2 71.445 6.986 32.318 1 38.39 ? O3P U5P 3250 E 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           21 
#