data_1XTU
#
_model_server_result.job_id            Pi9GAs7AEOVtjbagVvqBjg 
_model_server_result.datetime_utc      '2024-10-14 07:30:21' 
_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          1xtu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":6250}' 
#
_entry.id    1XTU 
#
_exptl.entry_id    1XTU 
_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    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         109 
_cell.angle_beta          90.76 
_cell.angle_gamma         115.4 
_cell.entry_id            1XTU 
_cell.length_a            71.67 
_cell.length_b            76.51 
_cell.length_c            91.45 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1XTU 
_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,D,E,H,I,J,N,O,P,Q,W,X 1 1 
B,C,F,G,K,L,M,R,S,T,U,V 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 K N N 
? 2 L N N 
? 2 N N N 
? 2 P N N 
? 2 R N N 
? 2 T N N 
? 2 W 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 361 n n 
N1 C6 U5P sing 362 n n 
N1 C1' U5P sing 363 n n 
C2 N3 U5P sing 364 n n 
C2 O2 U5P doub 365 n n 
N3 C4 U5P sing 366 n n 
N3 HN3 U5P sing 367 n n 
C4 C5 U5P sing 368 n n 
C4 O4 U5P doub 369 n n 
C5 C6 U5P doub 370 n n 
C5 H5 U5P sing 371 n n 
C6 H6 U5P sing 372 n n 
C1' C2' U5P sing 373 n n 
C1' O4' U5P sing 374 n n 
C1' H1' U5P sing 375 n n 
C2' O2' U5P sing 376 n n 
C2' C3' U5P sing 377 n n 
C2' H2' U5P sing 378 n n 
O2' HO2' U5P sing 379 n n 
C3' C4' U5P sing 380 n n 
C3' O3' U5P sing 381 n n 
C3' H3' U5P sing 382 n n 
C4' O4' U5P sing 383 n n 
C4' C5' U5P sing 384 n n 
C4' H4' U5P sing 385 n n 
O3' HO3' U5P sing 386 n n 
C5' O5' U5P sing 387 n n 
C5' "H5'1" U5P sing 388 n n 
C5' "H5'2" U5P sing 389 n n 
O5' P U5P sing 390 n n 
P O1P U5P doub 391 n n 
P O2P U5P sing 392 n n 
P O3P U5P sing 393 n n 
O2P HOP2 U5P sing 394 n n 
O3P HOP3 U5P sing 395 n n 
#
_atom_sites.entry_id                     1XTU 
_atom_sites.fract_transf_matrix[1][1]    0.013953 
_atom_sites.fract_transf_matrix[1][2]    0.006625 
_atom_sites.fract_transf_matrix[1][3]    0.002811 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014469 
_atom_sites.fract_transf_matrix[2][3]    0.005704 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.011755 
_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 U5P . 
J 3 CTP A 1 1260 260 CTP CTP . 
K 2 U5P B 1 2250 250 U5P U5P . 
L 2 U5P C 1 3250 250 U5P U5P . 
M 3 CTP C 1 3260 260 CTP CTP . 
N 2 U5P D 1 4250 250 U5P U5P . 
O 3 CTP D 1 4260 260 CTP CTP . 
P 2 U5P E 1 5250 250 U5P U5P . 
Q 3 CTP E 1 5260 260 CTP CTP . 
R 2 U5P F 1 6250 250 U5P U5P . 
S 3 CTP F 1 6260 260 CTP CTP . 
T 2 U5P G 1 7250 250 U5P U5P . 
U 3 CTP G 1 2260 260 CTP CTP . 
V 3 CTP G 1 7260 260 CTP CTP . 
W 2 U5P H 1 8250 250 U5P U5P . 
X 3 CTP H 1 8260 260 CTP CTP . 
#
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 . . . R 2 31.804 16.529 16.804 1 51.75 ? N1 U5P 6250 F 1 
HETATM 2 C C2 U5P . . . R 2 31.247 15.308 16.332 1 53.59 ? C2 U5P 6250 F 1 
HETATM 3 N N3 U5P . . . R 2 31.311 15.076 14.943 1 54.94 ? N3 U5P 6250 F 1 
HETATM 4 C C4 U5P . . . R 2 31.889 15.996 14.073 1 54.03 ? C4 U5P 6250 F 1 
HETATM 5 C C5 U5P . . . R 2 32.437 17.225 14.609 1 52.44 ? C5 U5P 6250 F 1 
HETATM 6 C C6 U5P . . . R 2 32.346 17.397 15.985 1 51.18 ? C6 U5P 6250 F 1 
HETATM 7 O O2 U5P . . . R 2 30.685 14.407 17.151 1 53.98 ? O2 U5P 6250 F 1 
HETATM 8 O O4 U5P . . . R 2 31.921 15.739 12.868 1 55.98 ? O4 U5P 6250 F 1 
HETATM 9 C C1' U5P . . . R 2 31.734 16.777 18.319 1 50.21 ? C1' U5P 6250 F 1 
HETATM 10 C C2' U5P . . . R 2 32.963 16.273 19.097 1 49.4 ? C2' U5P 6250 F 1 
HETATM 11 O O2' U5P . . . R 2 32.622 15.184 19.864 1 47.09 ? O2' U5P 6250 F 1 
HETATM 12 C C3' U5P . . . R 2 33.503 17.539 19.888 1 48.87 ? C3' U5P 6250 F 1 
HETATM 13 C C4' U5P . . . R 2 32.603 18.66 19.498 1 50.67 ? C4' U5P 6250 F 1 
HETATM 14 O O3' U5P . . . R 2 33.339 17.208 21.313 1 52.11 ? O3' U5P 6250 F 1 
HETATM 15 O O4' U5P . . . R 2 31.562 18.185 18.548 1 51.98 ? O4' U5P 6250 F 1 
HETATM 16 C C5' U5P . . . R 2 33.163 19.857 18.841 1 50.58 ? C5' U5P 6250 F 1 
HETATM 17 O O5' U5P . . . R 2 34.55 19.817 18.457 1 47.6 ? O5' U5P 6250 F 1 
HETATM 18 P P U5P . . . R 2 35.117 21.119 17.784 1 42.48 ? P U5P 6250 F 1 
HETATM 19 O O1P U5P . . . R 2 34.926 22.209 18.832 1 41.44 ? O1P U5P 6250 F 1 
HETATM 20 O O2P U5P . . . R 2 36.572 20.849 17.482 1 37.08 ? O2P U5P 6250 F 1 
HETATM 21 O O3P U5P . . . R 2 34.313 21.395 16.521 1 38.27 ? O3P U5P 6250 F 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           21 
#