data_7N7I
#
_model_server_result.job_id            0jCHQjjq6HcnIkCFxqifnA 
_model_server_result.datetime_utc      '2025-02-22 15:18:37' 
_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          7n7i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":403}' 
#
_entry.id    7N7I 
#
_exptl.entry_id    7N7I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              484.141 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE 5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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            7N7I 
_cell.length_a            85.943 
_cell.length_b            85.943 
_cell.length_c            111.718 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7N7I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        144 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F 1 1 
B,G,H,I 2 1 
C,J,K,L 3 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
? 4 F N N 
? 4 I N N 
? 4 L 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 D N SAM . A SAM 401 1_555 E FE2 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? 
metalc ? metalc2 D OXT SAM . A SAM 401 1_555 E FE2 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? 
metalc ? metalc3 G N SAM . B SAM 401 1_555 H FE2 SF4 . B SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
metalc ? metalc4 G OXT SAM . B SAM 401 1_555 H FE2 SF4 . B SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? 
metalc ? metalc5 J OXT SAM . C SAM 401 1_555 K FE2 SF4 . C SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
#
_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 419 n n 
PA O2A UTP sing 420 n n 
PA O3A UTP sing 421 n n 
PA O5' UTP sing 422 n n 
O2A H2A UTP sing 423 n n 
O3A PB UTP sing 424 n n 
O5' C5' UTP sing 425 n n 
PB O1B UTP sing 426 n n 
PB O2B UTP doub 427 n n 
PB O3B UTP sing 428 n n 
O1B H1B UTP sing 429 n n 
O3B PG UTP sing 430 n n 
PG O1G UTP sing 431 n n 
PG O2G UTP doub 432 n n 
PG O3G UTP sing 433 n n 
O1G H1G UTP sing 434 n n 
O3G H3G UTP sing 435 n n 
C5' C4' UTP sing 436 n n 
C5' "H5'1" UTP sing 437 n n 
C5' "H5'2" UTP sing 438 n n 
C4' O4' UTP sing 439 n n 
C4' C3' UTP sing 440 n n 
C4' H4' UTP sing 441 n n 
O4' C1' UTP sing 442 n n 
C1' C2' UTP sing 443 n n 
C1' N1 UTP sing 444 n n 
C1' H1' UTP sing 445 n n 
C2' O2' UTP sing 446 n n 
C2' C3' UTP sing 447 n n 
C2' H2' UTP sing 448 n n 
O2' HA UTP sing 449 n n 
C3' O3' UTP sing 450 n n 
C3' H3' UTP sing 451 n n 
O3' HB UTP sing 452 n n 
N1 C6 UTP sing 453 n y 
N1 C2 UTP sing 454 n y 
C6 C5 UTP doub 455 n y 
C6 H6 UTP sing 456 n n 
C2 O2 UTP doub 457 n n 
C2 N3 UTP sing 458 n y 
N3 C4 UTP sing 459 n y 
N3 H3 UTP sing 460 n n 
C4 O4 UTP doub 461 n n 
C4 C5 UTP sing 462 n y 
C5 H5 UTP sing 463 n n 
#
_atom_sites.entry_id                     7N7I 
_atom_sites.fract_transf_matrix[1][1]    0.011636 
_atom_sites.fract_transf_matrix[1][2]    0.006718 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013436 
_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]    0.008951 
_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
D 2 SAM A 1 401 304 SAM SAM . 
E 3 SF4 A 1 402 305 SF4 SF4 . 
F 4 UTP A 1 403 306 UTP UTP . 
G 2 SAM B 1 401 304 SAM SAM . 
H 3 SF4 B 1 402 305 SF4 SF4 . 
I 4 UTP B 1 403 306 UTP UTP . 
J 2 SAM C 1 401 304 SAM SAM . 
K 3 SF4 C 1 402 305 SF4 SF4 . 
L 4 UTP C 1 403 306 UTP UTP . 
#
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 . . . L 4 -48.184 -119.744 14.135 1 85.35 ? PA UTP 403 C 1 
HETATM 2 O O1A UTP . . . L 4 -48.461 -118.297 13.811 1 89.89 -1 O1A UTP 403 C 1 
HETATM 3 O O2A UTP . . . L 4 -47.489 -119.832 15.501 1 82.06 ? O2A UTP 403 C 1 
HETATM 4 O O3A UTP . . . L 4 -49.599 -120.587 14.181 1 92.18 ? O3A UTP 403 C 1 
HETATM 5 O O5' UTP . . . L 4 -47.184 -120.367 12.953 1 82.74 ? O5' UTP 403 C 1 
HETATM 6 P PB UTP . . . L 4 -50.925 -120.14 15.063 1 96.71 ? PB UTP 403 C 1 
HETATM 7 O O1B UTP . . . L 4 -51.864 -121.24 15.149 1 93.78 ? O1B UTP 403 C 1 
HETATM 8 O O2B UTP . . . L 4 -51.585 -118.982 14.403 1 97.39 -1 O2B UTP 403 C 1 
HETATM 9 O O3B UTP . . . L 4 -50.446 -119.699 16.603 1 89.89 ? O3B UTP 403 C 1 
HETATM 10 P PG UTP . . . L 4 -51.51 -119.162 17.78 1 84.22 ? PG UTP 403 C 1 
HETATM 11 O O1G UTP . . . L 4 -52.747 -120.04 17.771 1 84.17 ? O1G UTP 403 C 1 
HETATM 12 O O2G UTP . . . L 4 -51.89 -117.75 17.481 1 85.85 ? O2G UTP 403 C 1 
HETATM 13 O O3G UTP . . . L 4 -50.872 -119.226 19.113 1 83.97 ? O3G UTP 403 C 1 
HETATM 14 C C5' UTP . . . L 4 -46.511 -121.585 13.185 1 83.48 ? C5' UTP 403 C 1 
HETATM 15 C C4' UTP . . . L 4 -46.524 -122.355 12 1 82.52 ? C4' UTP 403 C 1 
HETATM 16 O O4' UTP . . . L 4 -45.317 -123.341 11.992 1 81.19 ? O4' UTP 403 C 1 
HETATM 17 C C1' UTP . . . L 4 -45.834 -124.455 11.471 1 82.62 ? C1' UTP 403 C 1 
HETATM 18 C C2' UTP . . . L 4 -47.347 -124.517 12.063 1 82.9 ? C2' UTP 403 C 1 
HETATM 19 O O2' UTP . . . L 4 -48.15 -125.406 11.283 1 79.02 ? O2' UTP 403 C 1 
HETATM 20 C C3' UTP . . . L 4 -47.799 -123.26 11.953 1 83.35 ? C3' UTP 403 C 1 
HETATM 21 O O3' UTP . . . L 4 -48.505 -123.087 10.695 1 83.37 ? O3' UTP 403 C 1 
HETATM 22 N N1 UTP . . . L 4 -45.07 -125.613 11.858 1 81.79 ? N1 UTP 403 C 1 
HETATM 23 C C6 UTP . . . L 4 -44.613 -125.714 13.089 1 81.91 ? C6 UTP 403 C 1 
HETATM 24 C C2 UTP . . . L 4 -44.816 -126.595 10.957 1 78.65 ? C2 UTP 403 C 1 
HETATM 25 O O2 UTP . . . L 4 -45.223 -126.506 9.829 1 73.42 ? O2 UTP 403 C 1 
HETATM 26 N N3 UTP . . . L 4 -44.092 -127.664 11.325 1 78.96 ? N3 UTP 403 C 1 
HETATM 27 C C4 UTP . . . L 4 -43.638 -127.764 12.566 1 80.43 ? C4 UTP 403 C 1 
HETATM 28 O O4 UTP . . . L 4 -43.013 -128.699 12.887 1 78.59 ? O4 UTP 403 C 1 
HETATM 29 C C5 UTP . . . L 4 -43.891 -126.795 13.458 1 81.59 ? C5 UTP 403 C 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           29 
#