data_8UV9
#
_model_server_result.job_id            8jFLhCj0mUqY4D_87o8JmQ 
_model_server_result.datetime_utc      '2025-07-30 20:44:22' 
_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          8uv9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":602}' 
#
_entry.id    8UV9 
#
_exptl.entry_id    8UV9 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              484.141 
_entity.id                          5 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            8UV9 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8UV9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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
? 5 H N N 
? 5 M N N 
? 5 P N N 
? 5 S N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 G MG MG . A MG 603 1_555 P O1B UTP . C UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc2 G MG MG . A MG 603 1_555 P O1A UTP . C UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc3 G MG MG . A MG 603 1_555 P O1G UTP . C UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? 
metalc ? metalc4 H O2A UTP . A UTP 604 1_555 I MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? 
metalc ? metalc5 H O2B UTP . A UTP 604 1_555 I MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc6 H O3G UTP . A UTP 604 1_555 I MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? 
metalc ? metalc7 L MG MG . B MG 603 1_555 S O2A UTP . D UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc8 L MG MG . B MG 603 1_555 S O2B UTP . D UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc9 L MG MG . B MG 603 1_555 S O3G UTP . D UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? 
metalc ? metalc10 M O1A UTP . B UTP 604 1_555 N MG MG . B MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc11 M O1B UTP . B UTP 604 1_555 N MG MG . B MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? 
metalc ? metalc12 M O1G UTP . B UTP 604 1_555 N MG MG . B MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? 
#
_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 392 n n 
PA O2A UTP sing 393 n n 
PA O3A UTP sing 394 n n 
PA O5' UTP sing 395 n n 
O2A H2A UTP sing 396 n n 
O3A PB UTP sing 397 n n 
O5' C5' UTP sing 398 n n 
PB O1B UTP sing 399 n n 
PB O2B UTP doub 400 n n 
PB O3B UTP sing 401 n n 
O1B H1B UTP sing 402 n n 
O3B PG UTP sing 403 n n 
PG O1G UTP sing 404 n n 
PG O2G UTP doub 405 n n 
PG O3G UTP sing 406 n n 
O1G H1G UTP sing 407 n n 
O3G H3G UTP sing 408 n n 
C5' C4' UTP sing 409 n n 
C5' "H5'1" UTP sing 410 n n 
C5' "H5'2" UTP sing 411 n n 
C4' O4' UTP sing 412 n n 
C4' C3' UTP sing 413 n n 
C4' H4' UTP sing 414 n n 
O4' C1' UTP sing 415 n n 
C1' C2' UTP sing 416 n n 
C1' N1 UTP sing 417 n n 
C1' H1' UTP sing 418 n n 
C2' O2' UTP sing 419 n n 
C2' C3' UTP sing 420 n n 
C2' H2' UTP sing 421 n n 
O2' HA UTP sing 422 n n 
C3' O3' UTP sing 423 n n 
C3' H3' UTP sing 424 n n 
O3' HB UTP sing 425 n n 
N1 C6 UTP sing 426 n y 
N1 C2 UTP sing 427 n y 
C6 C5 UTP doub 428 n y 
C6 H6 UTP sing 429 n n 
C2 O2 UTP doub 430 n n 
C2 N3 UTP sing 431 n y 
N3 C4 UTP sing 432 n y 
N3 H3 UTP sing 433 n n 
C4 O4 UTP doub 434 n n 
C4 C5 UTP sing 435 n y 
C5 H5 UTP sing 436 n n 
#
_atom_sites.entry_id                     8UV9 
_atom_sites.fract_transf_matrix[1][1]    1 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    1 
_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]    1 
_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 GLN A 1 601 611 GLN GLN . 
F 3 Q2N A 1 602 301 Q2N Q2N . 
G 4 MG A 1 603 4 MG MG . 
H 5 UTP A 1 604 602 UTP UTP . 
I 4 MG A 1 605 4 MG MG . 
J 2 GLN B 1 601 611 GLN GLN . 
K 3 Q2N B 1 602 301 Q2N Q2N . 
L 4 MG B 1 603 4 MG MG . 
M 5 UTP B 1 604 602 UTP UTP . 
N 4 MG B 1 605 4 MG MG . 
O 2 GLN C 1 601 611 GLN GLN . 
P 5 UTP C 1 602 602 UTP UTP . 
Q 3 Q2N C 1 603 301 Q2N Q2N . 
R 2 GLN D 1 601 611 GLN GLN . 
S 5 UTP D 1 602 602 UTP UTP . 
T 3 Q2N D 1 603 301 Q2N Q2N . 
#
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 . . . S 5 134.88 138.516 153.651 1 16.68 ? PA UTP 602 D 1 
HETATM 2 O O1A UTP . . . S 5 134.515 139.196 152.429 1 16.68 ? O1A UTP 602 D 1 
HETATM 3 O O2A UTP . . . S 5 133.677 137.754 153.932 1 16.68 ? O2A UTP 602 D 1 
HETATM 4 O O3A UTP . . . S 5 135.201 139.581 154.85 1 16.68 ? O3A UTP 602 D 1 
HETATM 5 O O5' UTP . . . S 5 136.207 137.591 153.388 1 16.68 ? O5' UTP 602 D 1 
HETATM 6 P PB UTP . . . S 5 134.565 139.476 156.35 1 16.68 ? PB UTP 602 D 1 
HETATM 7 O O1B UTP . . . S 5 135.59 139.205 157.335 1 16.68 ? O1B UTP 602 D 1 
HETATM 8 O O2B UTP . . . S 5 133.723 138.301 156.49 1 16.68 ? O2B UTP 602 D 1 
HETATM 9 O O3B UTP . . . S 5 133.737 140.846 156.704 1 16.68 ? O3B UTP 602 D 1 
HETATM 10 P PG UTP . . . S 5 132.352 141.302 155.955 1 16.68 ? PG UTP 602 D 1 
HETATM 11 O O1G UTP . . . S 5 131.355 141.811 156.869 1 16.68 ? O1G UTP 602 D 1 
HETATM 12 O O2G UTP . . . S 5 132.512 142.317 154.932 1 16.68 ? O2G UTP 602 D 1 
HETATM 13 O O3G UTP . . . S 5 131.65 140.248 155.256 1 16.68 ? O3G UTP 602 D 1 
HETATM 14 C C5' UTP . . . S 5 136.566 136.566 154.264 1 16.68 ? C5' UTP 602 D 1 
HETATM 15 C C4' UTP . . . S 5 137.555 135.703 153.548 1 16.68 ? C4' UTP 602 D 1 
HETATM 16 O O4' UTP . . . S 5 136.935 135.016 152.446 1 16.68 ? O4' UTP 602 D 1 
HETATM 17 C C1' UTP . . . S 5 137.913 134.881 151.383 1 16.68 ? C1' UTP 602 D 1 
HETATM 18 C C2' UTP . . . S 5 138.953 135.928 151.633 1 16.68 ? C2' UTP 602 D 1 
HETATM 19 O O2' UTP . . . S 5 140.232 135.309 151.726 1 16.68 ? O2' UTP 602 D 1 
HETATM 20 C C3' UTP . . . S 5 138.622 136.553 152.933 1 16.68 ? C3' UTP 602 D 1 
HETATM 21 O O3' UTP . . . S 5 139.771 136.582 153.775 1 16.68 ? O3' UTP 602 D 1 
HETATM 22 N N1 UTP . . . S 5 137.269 135.037 150.119 1 16.68 ? N1 UTP 602 D 1 
HETATM 23 C C6 UTP . . . S 5 137.432 134.05 148.898 1 16.68 ? C6 UTP 602 D 1 
HETATM 24 C C2 UTP . . . S 5 136.319 136.149 149.77 1 16.68 ? C2 UTP 602 D 1 
HETATM 25 O O2 UTP . . . S 5 136.088 136.973 150.579 1 16.68 ? O2 UTP 602 D 1 
HETATM 26 N N3 UTP . . . S 5 135.693 136.248 148.494 1 16.68 ? N3 UTP 602 D 1 
HETATM 27 C C4 UTP . . . S 5 135.905 135.365 147.54 1 16.68 ? C4 UTP 602 D 1 
HETATM 28 O O4 UTP . . . S 5 135.357 135.5 146.501 1 16.68 ? O4 UTP 602 D 1 
HETATM 29 C C5 UTP . . . S 5 136.793 134.24 147.744 1 16.68 ? C5 UTP 602 D 1 
HETATM 30 H "H5'1" UTP . . . S 5 135.693 135.988 154.55 1 16.68 ? "H5'1" UTP 602 D 1 
HETATM 31 H "H5'2" UTP . . . S 5 137.046 136.988 155.141 1 16.68 ? "H5'2" UTP 602 D 1 
HETATM 32 H H4' UTP . . . S 5 137.994 134.983 154.224 1 16.68 ? H4' UTP 602 D 1 
HETATM 33 H H1' UTP . . . S 5 138.37 133.901 151.44 1 16.68 ? H1' UTP 602 D 1 
HETATM 34 H H2' UTP . . . S 5 138.941 136.669 150.843 1 16.68 ? H2' UTP 602 D 1 
HETATM 35 H HA UTP . . . S 5 140.901 135.934 151.497 1 16.68 ? HA UTP 602 D 1 
HETATM 36 H H3' UTP . . . S 5 138.258 137.559 152.77 1 16.68 ? H3' UTP 602 D 1 
HETATM 37 H HB UTP . . . S 5 140.515 136.89 153.282 1 16.68 ? HB UTP 602 D 1 
HETATM 38 H H6 UTP . . . S 5 138.084 133.192 149.001 1 16.68 ? H6 UTP 602 D 1 
HETATM 39 H H3 UTP . . . S 5 135.073 137.014 148.316 1 16.68 ? H3 UTP 602 D 1 
HETATM 40 H H5 UTP . . . S 5 136.942 133.535 146.936 1 16.68 ? H5 UTP 602 D 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    37 
_model_server_stats.query_time_ms           378 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           40 
#