data_1V34 # _model_server_result.job_id T_2WBee1SsSAkmmCMRpuxQ _model_server_result.datetime_utc '2025-02-27 01:15:08' _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 1v34 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":3000}' # _entry.id 1V34 # _exptl.entry_id 1V34 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 1V34 _cell.length_a 76.386 _cell.length_b 76.386 _cell.length_c 128.83 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1V34 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 SG CYS 126 A CYS 106 1_555 B ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc2 A NE2 HIS 128 A HIS 108 1_555 B ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc3 A SG CYS 134 A CYS 114 1_555 B ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc4 A SG CYS 137 A CYS 117 1_555 B ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? # _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 1V34 _atom_sites.fract_transf_matrix[1][1] 0.013091 _atom_sites.fract_transf_matrix[1][2] 0.007558 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015117 _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] 0.007762 _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 B 2 ZN A 1 1000 1000 ZN ZN . C 3 UTP A 1 3000 3000 UTP UTP . D 4 HOH A 1 2001 2001 HOH TIP . D 4 HOH A 2 2002 2002 HOH TIP . D 4 HOH A 3 4001 4001 HOH TIP . D 4 HOH A 4 4002 4002 HOH TIP . D 4 HOH A 5 4003 4003 HOH TIP . D 4 HOH A 6 4004 4004 HOH TIP . D 4 HOH A 7 4005 4005 HOH TIP . D 4 HOH A 8 4006 4006 HOH TIP . D 4 HOH A 9 4007 4007 HOH TIP . D 4 HOH A 10 4008 4008 HOH TIP . D 4 HOH A 11 4009 4009 HOH TIP . D 4 HOH A 12 4010 4010 HOH TIP . D 4 HOH A 13 4011 4011 HOH TIP . D 4 HOH A 14 4012 4012 HOH TIP . D 4 HOH A 15 4013 4013 HOH TIP . D 4 HOH A 16 4014 4014 HOH TIP . D 4 HOH A 17 4015 4015 HOH TIP . D 4 HOH A 18 4016 4016 HOH TIP . D 4 HOH A 19 4017 4017 HOH TIP . D 4 HOH A 20 4018 4018 HOH TIP . D 4 HOH A 21 4019 4019 HOH TIP . # 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 . . . C 3 29.706 42.746 14.417 1 96.01 ? PA UTP 3000 A 1 HETATM 2 O O1A UTP . . . C 3 29.077 44.089 14.523 1 95.92 ? O1A UTP 3000 A 1 HETATM 3 O O2A UTP . . . C 3 29.268 41.662 15.338 1 95.24 ? O2A UTP 3000 A 1 HETATM 4 O O3A UTP . . . C 3 31.329 42.872 14.537 1 88.3 ? O3A UTP 3000 A 1 HETATM 5 O O5' UTP . . . C 3 29.636 42.206 12.922 1 103.45 ? O5' UTP 3000 A 1 HETATM 6 P PB UTP . . . C 3 32.267 42.979 15.799 1 80.54 ? PB UTP 3000 A 1 HETATM 7 O O1B UTP . . . C 3 33.134 44.129 15.86 1 80.89 ? O1B UTP 3000 A 1 HETATM 8 O O2B UTP . . . C 3 32.901 41.684 15.855 1 80.56 ? O2B UTP 3000 A 1 HETATM 9 O O3B UTP . . . C 3 31.123 43.149 16.876 1 81.65 ? O3B UTP 3000 A 1 HETATM 10 P PG UTP . . . C 3 31.137 43.32 18.431 1 79.44 ? PG UTP 3000 A 1 HETATM 11 O O1G UTP . . . C 3 31.98 42.179 19.002 1 81.6 ? O1G UTP 3000 A 1 HETATM 12 O O2G UTP . . . C 3 31.727 44.684 18.647 1 82.11 ? O2G UTP 3000 A 1 HETATM 13 O O3G UTP . . . C 3 29.703 43.233 18.899 1 82.45 ? O3G UTP 3000 A 1 HETATM 14 C C5' UTP . . . C 3 30.189 40.938 12.604 1 117.72 ? C5' UTP 3000 A 1 HETATM 15 C C4' UTP . . . C 3 29.369 40.221 11.572 1 128.12 ? C4' UTP 3000 A 1 HETATM 16 O O4' UTP . . . C 3 29.958 40.471 10.262 1 132.07 ? O4' UTP 3000 A 1 HETATM 17 C C1' UTP . . . C 3 30.058 39.273 9.516 1 134.39 ? C1' UTP 3000 A 1 HETATM 18 C C2' UTP . . . C 3 29.978 38.109 10.532 1 134.13 ? C2' UTP 3000 A 1 HETATM 19 O O2' UTP . . . C 3 29.263 37.007 10.017 1 135.99 ? O2' UTP 3000 A 1 HETATM 20 C C3' UTP . . . C 3 29.352 38.716 11.798 1 130.91 ? C3' UTP 3000 A 1 HETATM 21 O O3' UTP . . . C 3 28.002 38.277 11.999 1 131.12 ? O3' UTP 3000 A 1 HETATM 22 N N1 UTP . . . C 3 31.342 39.284 8.713 1 135.07 ? N1 UTP 3000 A 1 HETATM 23 C C6 UTP . . . C 3 31.32 38.934 7.357 1 134.79 ? C6 UTP 3000 A 1 HETATM 24 C C2 UTP . . . C 3 32.582 39.647 9.339 1 134.66 ? C2 UTP 3000 A 1 HETATM 25 O O2 UTP . . . C 3 32.688 39.966 10.518 1 134.45 ? O2 UTP 3000 A 1 HETATM 26 N N3 UTP . . . C 3 33.691 39.616 8.494 1 133.76 ? N3 UTP 3000 A 1 HETATM 27 C C4 UTP . . . C 3 33.718 39.272 7.134 1 133.43 ? C4 UTP 3000 A 1 HETATM 28 O O4 UTP . . . C 3 34.797 39.293 6.521 1 133.41 ? O4 UTP 3000 A 1 HETATM 29 C C5 UTP . . . C 3 32.429 38.916 6.569 1 133.1 ? C5 UTP 3000 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 29 #