data_4E80
#
_model_server_result.job_id            4YXHuq6yt-6-iFEPxk93OQ 
_model_server_result.datetime_utc      '2025-08-29 20:57:05' 
_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          4e80 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":501}' 
#
_entry.id    4E80 
#
_exptl.entry_id    4E80 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              484.141 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE 5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          109.29 
_cell.angle_gamma         90 
_cell.entry_id            4E80 
_cell.length_a            164.69 
_cell.length_b            77.96 
_cell.length_c            151.68 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4E80 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,I 1 1 
B,F,J 2 1 
C,G,K 3 1 
D,H,L 4 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 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
#
_chem_comp.formula           'C9 H15 N2 O15 P3' 
_chem_comp.formula_weight    484.141 
_chem_comp.id                UTP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE 5'-TRIPHOSPHATE" 
_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
PA O1A UTP doub 358 n n 
PA O2A UTP sing 359 n n 
PA O3A UTP sing 360 n n 
PA O5' UTP sing 361 n n 
O2A H2A UTP sing 362 n n 
O3A PB UTP sing 363 n n 
O5' C5' UTP sing 364 n n 
PB O1B UTP sing 365 n n 
PB O2B UTP doub 366 n n 
PB O3B UTP sing 367 n n 
O1B H1B UTP sing 368 n n 
O3B PG UTP sing 369 n n 
PG O1G UTP sing 370 n n 
PG O2G UTP doub 371 n n 
PG O3G UTP sing 372 n n 
O1G H1G UTP sing 373 n n 
O3G H3G UTP sing 374 n n 
C5' C4' UTP sing 375 n n 
C5' "H5'1" UTP sing 376 n n 
C5' "H5'2" UTP sing 377 n n 
C4' O4' UTP sing 378 n n 
C4' C3' UTP sing 379 n n 
C4' H4' UTP sing 380 n n 
O4' C1' UTP sing 381 n n 
C1' C2' UTP sing 382 n n 
C1' N1 UTP sing 383 n n 
C1' H1' UTP sing 384 n n 
C2' O2' UTP sing 385 n n 
C2' C3' UTP sing 386 n n 
C2' H2' UTP sing 387 n n 
O2' HA UTP sing 388 n n 
C3' O3' UTP sing 389 n n 
C3' H3' UTP sing 390 n n 
O3' HB UTP sing 391 n n 
N1 C6 UTP sing 392 n y 
N1 C2 UTP sing 393 n y 
C6 C5 UTP doub 394 n y 
C6 H6 UTP sing 395 n n 
C2 O2 UTP doub 396 n n 
C2 N3 UTP sing 397 n y 
N3 C4 UTP sing 398 n y 
N3 H3 UTP sing 399 n n 
C4 O4 UTP doub 400 n n 
C4 C5 UTP sing 401 n y 
C5 H5 UTP sing 402 n n 
#
_atom_sites.entry_id                     4E80 
_atom_sites.fract_transf_matrix[1][1]    0.006072 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002125 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012827 
_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]    0.006985 
_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
E 2 UTP A 1 501 501 UTP UTP . 
F 2 UTP B 1 501 501 UTP UTP . 
G 2 UTP C 1 501 501 UTP UTP . 
H 2 UTP D 1 500 500 UTP UTP . 
I 3 HOH A 1 601 6 HOH HOH . 
I 3 HOH A 2 602 7 HOH HOH . 
I 3 HOH A 3 603 8 HOH HOH . 
J 3 HOH B 1 601 3 HOH HOH . 
J 3 HOH B 2 602 4 HOH HOH . 
J 3 HOH B 3 603 5 HOH HOH . 
J 3 HOH B 4 604 9 HOH HOH . 
J 3 HOH B 5 605 10 HOH HOH . 
J 3 HOH B 6 606 11 HOH HOH . 
J 3 HOH B 7 607 12 HOH HOH . 
K 3 HOH C 1 601 2 HOH HOH . 
K 3 HOH C 2 602 14 HOH HOH . 
L 3 HOH D 1 601 1 HOH HOH . 
L 3 HOH D 2 602 13 HOH HOH . 
L 3 HOH D 3 603 15 HOH HOH . 
L 3 HOH D 4 604 16 HOH HOH . 
L 3 HOH D 5 605 17 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 P PA UTP . . . F 2 20.409 -36.007 56.253 1 46.79 ? PA UTP 501 B 1 
HETATM 2 O O1A UTP . . . F 2 21.74 -35.57 56.752 1 48.2 ? O1A UTP 501 B 1 
HETATM 3 O O2A UTP . . . F 2 20.284 -35.685 54.679 1 44.8 ? O2A UTP 501 B 1 
HETATM 4 O O3A UTP . . . F 2 20.208 -37.56 56.472 1 52.71 ? O3A UTP 501 B 1 
HETATM 5 O O5' UTP . . . F 2 19.134 -35.402 57.006 1 46.1 ? O5' UTP 501 B 1 
HETATM 6 P PB UTP . . . F 2 20.385 -37.958 58.075 1 54.44 ? PB UTP 501 B 1 
HETATM 7 O O1B UTP . . . F 2 21.037 -36.789 58.985 1 55.32 ? O1B UTP 501 B 1 
HETATM 8 O O2B UTP . . . F 2 19.034 -38.267 58.63 1 53.4 ? O2B UTP 501 B 1 
HETATM 9 O O3B UTP . . . F 2 21.289 -39.315 58.163 1 55.31 ? O3B UTP 501 B 1 
HETATM 10 P PG UTP . . . F 2 22.901 -39.056 58.207 1 54.04 ? PG UTP 501 B 1 
HETATM 11 O O1G UTP . . . F 2 23.607 -39.902 57.046 1 49.5 ? O1G UTP 501 B 1 
HETATM 12 O O2G UTP . . . F 2 23.402 -39.53 59.526 1 55.81 ? O2G UTP 501 B 1 
HETATM 13 O O3G UTP . . . F 2 23.284 -37.497 58.002 1 58.31 ? O3G UTP 501 B 1 
HETATM 14 C C5' UTP . . . F 2 19.266 -34.037 57.087 1 41.44 ? C5' UTP 501 B 1 
HETATM 15 C C4' UTP . . . F 2 18.034 -33.447 57.708 1 38.48 ? C4' UTP 501 B 1 
HETATM 16 O O4' UTP . . . F 2 17.795 -32.178 57.115 1 40.68 ? O4' UTP 501 B 1 
HETATM 17 C C1' UTP . . . F 2 16.456 -32.115 56.618 1 40.63 ? C1' UTP 501 B 1 
HETATM 18 C C2' UTP . . . F 2 15.688 -33.305 57.188 1 38.75 ? C2' UTP 501 B 1 
HETATM 19 O O2' UTP . . . F 2 14.794 -32.853 58.212 1 39.83 ? O2' UTP 501 B 1 
HETATM 20 C C3' UTP . . . F 2 16.724 -34.279 57.77 1 38.32 ? C3' UTP 501 B 1 
HETATM 21 O O3' UTP . . . F 2 16.384 -34.615 59.099 1 43.43 ? O3' UTP 501 B 1 
HETATM 22 N N1 UTP . . . F 2 16.438 -32.229 55.158 1 40.97 ? N1 UTP 501 B 1 
HETATM 23 C C6 UTP . . . F 2 17.472 -32.857 54.501 1 39.63 ? C6 UTP 501 B 1 
HETATM 24 C C2 UTP . . . F 2 15.385 -31.727 54.473 1 43.78 ? C2 UTP 501 B 1 
HETATM 25 O O2 UTP . . . F 2 14.482 -31.169 55.092 1 45.47 ? O2 UTP 501 B 1 
HETATM 26 N N3 UTP . . . F 2 15.324 -31.843 53.112 1 42.23 ? N3 UTP 501 B 1 
HETATM 27 C C4 UTP . . . F 2 16.329 -32.464 52.438 1 40.47 ? C4 UTP 501 B 1 
HETATM 28 O O4 UTP . . . F 2 16.287 -32.587 51.229 1 40.39 ? O4 UTP 501 B 1 
HETATM 29 C C5 UTP . . . F 2 17.44 -32.982 53.156 1 40.04 ? C5 UTP 501 B 1 
#
_model_server_stats.io_time_ms              35 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    96 
_model_server_stats.query_time_ms           716 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           29 
#