data_4BPW
#
_model_server_result.job_id            j8mHen2SmanUcPxqqz7-aw 
_model_server_result.datetime_utc      '2024-12-12 12:10:24' 
_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          4bpw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":1412}' 
#
_entry.id    4BPW 
#
_exptl.entry_id    4BPW 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          104.9 
_cell.angle_gamma         90 
_cell.entry_id            4BPW 
_cell.length_a            116.394 
_cell.length_b            69.438 
_cell.length_c            127.087 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4BPW 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 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 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 
PISA monomeric 1 author_and_software_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,F,G,H 1 1 
C,I,J,K,L 2 1 
B 3 1 
D 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
? 5 H N N 
? 5 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 A OD2 ASP 112 A ASP 109 1_555 F MG MG . A MG 1412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? 
metalc ? metalc2 A OD1 ASP 112 A ASP 109 1_555 G MG MG . A MG 1413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? 
metalc ? metalc3 A OD1 ASP 114 A ASP 111 1_555 G MG MG . A MG 1413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc4 A SG CYS 124 A CYS 121 1_555 E ZN ZN . A ZN 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc5 A SG CYS 125 A CYS 122 1_555 E ZN ZN . A ZN 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc6 A SG CYS 131 A CYS 128 1_555 E ZN ZN . A ZN 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc7 A SG CYS 134 A CYS 131 1_555 E ZN ZN . A ZN 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
metalc ? metalc8 A OD2 ASP 309 A ASP 306 1_555 F MG MG . A MG 1412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? 
metalc ? metalc9 G MG MG . A MG 1413 1_555 H O2G UTP . A UTP 1414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc10 G MG MG . A MG 1413 1_555 H O2B UTP . A UTP 1414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? 
metalc ? metalc11 C OD2 ASP 112 C ASP 109 1_555 J MG MG . C MG 1410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? 
metalc ? metalc12 C OD2 ASP 114 C ASP 111 1_555 K MG MG . C MG 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? 
metalc ? metalc13 C SG CYS 124 C CYS 121 1_555 I ZN ZN . C ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc14 C SG CYS 125 C CYS 122 1_555 I ZN ZN . C ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc15 C SG CYS 131 C CYS 128 1_555 I ZN ZN . C ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc16 C SG CYS 134 C CYS 131 1_555 I ZN ZN . C ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc17 K MG MG . C MG 1411 1_555 L O2G UTP . C UTP 1412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? 
metalc ? metalc18 K MG MG . C MG 1411 1_555 L O2B UTP . C UTP 1412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? 
#
_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 356 n n 
PA O2A UTP sing 357 n n 
PA O3A UTP sing 358 n n 
PA O5' UTP sing 359 n n 
O2A H2A UTP sing 360 n n 
O3A PB UTP sing 361 n n 
O5' C5' UTP sing 362 n n 
PB O1B UTP sing 363 n n 
PB O2B UTP doub 364 n n 
PB O3B UTP sing 365 n n 
O1B H1B UTP sing 366 n n 
O3B PG UTP sing 367 n n 
PG O1G UTP sing 368 n n 
PG O2G UTP doub 369 n n 
PG O3G UTP sing 370 n n 
O1G H1G UTP sing 371 n n 
O3G H3G UTP sing 372 n n 
C5' C4' UTP sing 373 n n 
C5' "H5'1" UTP sing 374 n n 
C5' "H5'2" UTP sing 375 n n 
C4' O4' UTP sing 376 n n 
C4' C3' UTP sing 377 n n 
C4' H4' UTP sing 378 n n 
O4' C1' UTP sing 379 n n 
C1' C2' UTP sing 380 n n 
C1' N1 UTP sing 381 n n 
C1' H1' UTP sing 382 n n 
C2' O2' UTP sing 383 n n 
C2' C3' UTP sing 384 n n 
C2' H2' UTP sing 385 n n 
O2' HA UTP sing 386 n n 
C3' O3' UTP sing 387 n n 
C3' H3' UTP sing 388 n n 
O3' HB UTP sing 389 n n 
N1 C6 UTP sing 390 n y 
N1 C2 UTP sing 391 n y 
C6 C5 UTP doub 392 n y 
C6 H6 UTP sing 393 n n 
C2 O2 UTP doub 394 n n 
C2 N3 UTP sing 395 n y 
N3 C4 UTP sing 396 n y 
N3 H3 UTP sing 397 n n 
C4 O4 UTP doub 398 n n 
C4 C5 UTP sing 399 n y 
C5 H5 UTP sing 400 n n 
#
_atom_sites.entry_id                     4BPW 
_atom_sites.fract_transf_matrix[1][1]    0.008592 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002286 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014401 
_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]    0.008142 
_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 3 ZN A 1 1411 1411 ZN ZN . 
F 4 MG A 1 1412 1412 MG MG . 
G 4 MG A 1 1413 1413 MG MG . 
H 5 UTP A 1 1414 1414 UTP UTP . 
I 3 ZN C 1 1409 1409 ZN ZN . 
J 4 MG C 1 1410 1410 MG MG . 
K 4 MG C 1 1411 1411 MG MG . 
L 5 UTP C 1 1412 1412 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 5 -0.766 54.835 46.901 0.68 125.15 ? PA UTP 1412 C 1 
HETATM 2 O O1A UTP . . . L 5 -0.736 53.536 46.161 0.68 129.05 ? O1A UTP 1412 C 1 
HETATM 3 O O2A UTP . . . L 5 0.538 55.024 47.627 0.68 100.76 ? O2A UTP 1412 C 1 
HETATM 4 O O3A UTP . . . L 5 -1.98 54.776 47.955 0.68 111.82 ? O3A UTP 1412 C 1 
HETATM 5 O O5' UTP . . . L 5 -0.973 56.013 45.876 0.68 121.03 ? O5' UTP 1412 C 1 
HETATM 6 P PB UTP . . . L 5 -3.167 55.86 48.115 0.68 100.03 ? PB UTP 1412 C 1 
HETATM 7 O O1B UTP . . . L 5 -3.991 55.902 46.827 0.68 100.47 ? O1B UTP 1412 C 1 
HETATM 8 O O2B UTP . . . L 5 -2.602 57.241 48.407 0.68 90.4 ? O2B UTP 1412 C 1 
HETATM 9 O O3B UTP . . . L 5 -4.088 55.383 49.319 0.68 112.01 ? O3B UTP 1412 C 1 
HETATM 10 P PG UTP . . . L 5 -3.521 54.921 50.732 0.68 109.33 ? PG UTP 1412 C 1 
HETATM 11 O O1G UTP . . . L 5 -4.031 55.851 51.814 0.68 92.63 ? O1G UTP 1412 C 1 
HETATM 12 O O2G UTP . . . L 5 -2 54.967 50.71 0.68 104.93 ? O2G UTP 1412 C 1 
HETATM 13 O O3G UTP . . . L 5 -3.97 53.518 51.011 0.68 88.81 ? O3G UTP 1412 C 1 
HETATM 14 C C5' UTP . . . L 5 -0.197 56.029 44.703 0.68 111.8 ? C5' UTP 1412 C 1 
HETATM 15 C C4' UTP . . . L 5 -1.05 56.544 43.557 0.68 117.41 ? C4' UTP 1412 C 1 
HETATM 16 O O4' UTP . . . L 5 -0.608 56.076 42.321 0.68 121.46 ? O4' UTP 1412 C 1 
HETATM 17 C C1' UTP . . . L 5 -1.618 56.137 41.391 0.68 122.02 ? C1' UTP 1412 C 1 
HETATM 18 C C2' UTP . . . L 5 -2.848 55.806 42.182 0.68 122.92 ? C2' UTP 1412 C 1 
HETATM 19 O O2' UTP . . . L 5 -3.909 56.68 41.83 0.68 114.34 ? O2' UTP 1412 C 1 
HETATM 20 C C3' UTP . . . L 5 -2.445 56.021 43.633 0.68 126.11 ? C3' UTP 1412 C 1 
HETATM 21 O O3' UTP . . . L 5 -3.286 56.951 44.235 0.68 127.34 ? O3' UTP 1412 C 1 
HETATM 22 N N1 UTP . . . L 5 -1.451 55.235 40.278 0.68 124.4 ? N1 UTP 1412 C 1 
HETATM 23 C C6 UTP . . . L 5 -1.668 55.715 39.036 0.68 122.86 ? C6 UTP 1412 C 1 
HETATM 24 C C2 UTP . . . L 5 -1.091 53.915 40.443 0.68 125.14 ? C2 UTP 1412 C 1 
HETATM 25 O O2 UTP . . . L 5 -0.893 53.459 41.555 0.68 128.09 ? O2 UTP 1412 C 1 
HETATM 26 N N3 UTP . . . L 5 -0.954 53.116 39.361 0.68 131.71 ? N3 UTP 1412 C 1 
HETATM 27 C C4 UTP . . . L 5 -1.17 53.605 38.117 0.68 129.97 ? C4 UTP 1412 C 1 
HETATM 28 O O4 UTP . . . L 5 -1.048 52.896 37.162 0.68 127.09 ? O4 UTP 1412 C 1 
HETATM 29 C C5 UTP . . . L 5 -1.532 54.92 37.953 0.68 120.15 ? C5 UTP 1412 C 1 
HETATM 30 H "H5'1" UTP . . . L 5 0.109 55.111 44.497 0.68 134.16 ? "H5'1" UTP 1412 C 1 
HETATM 31 H "H5'2" UTP . . . L 5 0.576 56.611 44.829 0.68 134.16 ? "H5'2" UTP 1412 C 1 
HETATM 32 H H4' UTP . . . L 5 -1.059 57.522 43.56 0.68 140.89 ? H4' UTP 1412 C 1 
HETATM 33 H H1' UTP . . . L 5 -1.69 57.057 41.052 0.68 146.43 ? H1' UTP 1412 C 1 
HETATM 34 H H2' UTP . . . L 5 -3.108 54.876 42.035 0.68 147.51 ? H2' UTP 1412 C 1 
HETATM 35 H HA UTP . . . L 5 -4.619 56.202 41.586 0.68 137.21 ? HA UTP 1412 C 1 
HETATM 36 H H3' UTP . . . L 5 -2.466 55.177 44.121 0.68 151.33 ? H3' UTP 1412 C 1 
HETATM 37 H HB UTP . . . L 5 -4.112 56.616 44.288 0.68 152.81 ? HB UTP 1412 C 1 
HETATM 38 H H6 UTP . . . L 5 -1.921 56.638 38.92 0.68 147.44 ? H6 UTP 1412 C 1 
HETATM 39 H H3 UTP . . . L 5 -0.713 52.24 39.471 0.68 158.06 ? H3 UTP 1412 C 1 
HETATM 40 H H5 UTP . . . L 5 -1.692 55.285 37.043 0.68 144.18 ? H5 UTP 1412 C 1 
#
_model_server_stats.io_time_ms              130 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           40 
#