data_4BPW # _model_server_result.job_id 6TGueSKzUgL9G3AD_Qcvxw _model_server_result.datetime_utc '2024-11-07 10:29:14' _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":"H","auth_seq_id":1414}' # _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 . . . H 5 44.375 64.657 -11.863 0.69 69.68 ? PA UTP 1414 A 1 HETATM 2 O O1A UTP . . . H 5 44.088 65.796 -10.932 0.69 56.38 ? O1A UTP 1414 A 1 HETATM 3 O O2A UTP . . . H 5 45.059 63.539 -11.121 0.69 69.82 ? O2A UTP 1414 A 1 HETATM 4 O O3A UTP . . . H 5 45.334 65.163 -13.05 0.69 46.36 ? O3A UTP 1414 A 1 HETATM 5 O O5' UTP . . . H 5 43.048 64.102 -12.501 0.69 43.87 ? O5' UTP 1414 A 1 HETATM 6 P PB UTP . . . H 5 45.147 64.684 -14.576 0.69 37.44 ? PB UTP 1414 A 1 HETATM 7 O O1B UTP . . . H 5 44.085 65.546 -15.267 0.69 30.21 ? O1B UTP 1414 A 1 HETATM 8 O O2B UTP . . . H 5 44.71 63.233 -14.576 0.69 48.36 ? O2B UTP 1414 A 1 HETATM 9 O O3B UTP . . . H 5 46.518 64.832 -15.361 0.69 40.58 ? O3B UTP 1414 A 1 HETATM 10 P PG UTP . . . H 5 47.94 64.425 -14.783 0.69 40.95 ? PG UTP 1414 A 1 HETATM 11 O O1G UTP . . . H 5 48.684 63.518 -15.744 0.69 36.46 ? O1G UTP 1414 A 1 HETATM 12 O O2G UTP . . . H 5 47.733 63.689 -13.469 0.69 49.74 ? O2G UTP 1414 A 1 HETATM 13 O O3G UTP . . . H 5 48.728 65.686 -14.579 0.69 37.04 ? O3G UTP 1414 A 1 HETATM 14 C C5' UTP . . . H 5 41.833 64.217 -11.807 0.69 53.52 ? C5' UTP 1414 A 1 HETATM 15 C C4' UTP . . . H 5 40.856 65.019 -12.645 0.69 59.89 ? C4' UTP 1414 A 1 HETATM 16 O O4' UTP . . . H 5 39.992 65.692 -11.792 0.69 56.01 ? O4' UTP 1414 A 1 HETATM 17 C C1' UTP . . . H 5 39.457 66.809 -12.362 0.69 50.76 ? C1' UTP 1414 A 1 HETATM 18 C C2' UTP . . . H 5 40.411 67.192 -13.465 0.69 44.11 ? C2' UTP 1414 A 1 HETATM 19 O O2' UTP . . . H 5 39.758 67.132 -14.721 0.69 43.28 ? O2' UTP 1414 A 1 HETATM 20 C C3' UTP . . . H 5 41.494 66.125 -13.413 0.69 52.7 ? C3' UTP 1414 A 1 HETATM 21 O O3' UTP . . . H 5 41.835 65.711 -14.694 0.69 28.98 ? O3' UTP 1414 A 1 HETATM 22 N N1 UTP . . . H 5 39.18 67.818 -11.366 0.69 56.52 ? N1 UTP 1414 A 1 HETATM 23 C C6 UTP . . . H 5 37.883 68.042 -11.051 0.69 46.35 ? C6 UTP 1414 A 1 HETATM 24 C C2 UTP . . . H 5 40.174 68.528 -10.713 0.69 66.65 ? C2 UTP 1414 A 1 HETATM 25 O O2 UTP . . . H 5 41.352 68.346 -10.966 0.69 71.58 ? O2 UTP 1414 A 1 HETATM 26 N N3 UTP . . . H 5 39.841 69.449 -9.779 0.69 57.73 ? N3 UTP 1414 A 1 HETATM 27 C C4 UTP . . . H 5 38.541 69.675 -9.474 0.69 60.59 ? C4 UTP 1414 A 1 HETATM 28 O O4 UTP . . . H 5 38.256 70.492 -8.645 0.69 71.63 ? O4 UTP 1414 A 1 HETATM 29 C C5 UTP . . . H 5 37.552 68.963 -10.117 0.69 50.55 ? C5 UTP 1414 A 1 HETATM 30 H "H5'1" UTP . . . H 5 41.986 64.675 -10.944 0.69 64.22 ? "H5'1" UTP 1414 A 1 HETATM 31 H "H5'2" UTP . . . H 5 41.468 63.328 -11.644 0.69 64.22 ? "H5'2" UTP 1414 A 1 HETATM 32 H H4' UTP . . . H 5 40.355 64.43 -13.245 0.69 71.86 ? H4' UTP 1414 A 1 HETATM 33 H H1' UTP . . . H 5 38.602 66.558 -12.778 0.69 60.92 ? H1' UTP 1414 A 1 HETATM 34 H H2' UTP . . . H 5 40.788 68.08 -13.308 0.69 52.94 ? H2' UTP 1414 A 1 HETATM 35 H HA UTP . . . H 5 39.718 67.948 -15.075 0.69 51.94 ? HA UTP 1414 A 1 HETATM 36 H H3' UTP . . . H 5 42.279 66.459 -12.942 0.69 63.24 ? H3' UTP 1414 A 1 HETATM 37 H HB UTP . . . H 5 41.098 65.467 -15.135 0.69 34.78 ? HB UTP 1414 A 1 HETATM 38 H H6 UTP . . . H 5 37.189 67.545 -11.499 0.69 55.62 ? H6 UTP 1414 A 1 HETATM 39 H H3 UTP . . . H 5 40.498 69.922 -9.352 0.69 69.27 ? H3 UTP 1414 A 1 HETATM 40 H H5 UTP . . . H 5 36.597 69.127 -9.896 0.69 60.66 ? H5 UTP 1414 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #