data_5LVV # _model_server_result.job_id xKfrqCQRODV5e42r23eXKQ _model_server_result.datetime_utc '2024-11-06 15:24:20' _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 5lvv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1201}' # _entry.id 5LVV # _exptl.entry_id 5LVV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 5LVV _cell.length_a 98.533 _cell.length_b 98.533 _cell.length_c 367.2 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LVV _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id OG _struct_conn.ptnr1_label_comp_id SER _struct_conn.ptnr1_label_seq_id 10 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id SER _struct_conn.ptnr1_auth_seq_id 297 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id C1 _struct_conn.ptnr2_label_comp_id NAG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id NAG _struct_conn.ptnr2_auth_seq_id 1202 _struct_conn.ptnr2_symmetry 1_555 _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 1.228 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 N1 C2 UDP sing 388 n n N1 C6 UDP sing 389 n n N1 C1' UDP sing 390 n n C2 N3 UDP sing 391 n n C2 O2 UDP doub 392 n n N3 C4 UDP sing 393 n n N3 HN3 UDP sing 394 n n C4 C5 UDP sing 395 n n C4 O4 UDP doub 396 n n C5 C6 UDP doub 397 n n C5 H5 UDP sing 398 n n C6 H6 UDP sing 399 n n C1' C2' UDP sing 400 n n C1' O4' UDP sing 401 n n C1' H1' UDP sing 402 n n C2' O2' UDP sing 403 n n C2' C3' UDP sing 404 n n C2' H2' UDP sing 405 n n O2' HO2' UDP sing 406 n n C3' C4' UDP sing 407 n n C3' O3' UDP sing 408 n n C3' H3' UDP sing 409 n n C4' O4' UDP sing 410 n n C4' C5' UDP sing 411 n n C4' H4' UDP sing 412 n n O3' HO3' UDP sing 413 n n C5' O5' UDP sing 414 n n C5' "H5'1" UDP sing 415 n n C5' "H5'2" UDP sing 416 n n O5' PA UDP sing 417 n n PA O1A UDP doub 418 n n PA O2A UDP sing 419 n n PA O3A UDP sing 420 n n O2A HOA2 UDP sing 421 n n O3A PB UDP sing 422 n n PB O1B UDP doub 423 n n PB O2B UDP sing 424 n n PB O3B UDP sing 425 n n O2B HOB2 UDP sing 426 n n O3B HOB3 UDP sing 427 n n # _atom_sites.entry_id 5LVV _atom_sites.fract_transf_matrix[1][1] 0.010149 _atom_sites.fract_transf_matrix[1][2] 0.005859 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011719 _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] 0.002723 _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 UDP A 1 1201 1201 UDP UDP . C 3 NAG A 1 1202 1202 NAG NAG . D 3 NAG A 1 1203 1203 NAG NAG . E 3 NAG A 1 1204 1204 NAG NAG . F 4 HOH A 1 1301 21 HOH HOH . F 4 HOH A 2 1302 25 HOH HOH . F 4 HOH A 3 1303 35 HOH HOH . F 4 HOH A 4 1304 2 HOH HOH . F 4 HOH A 5 1305 19 HOH HOH . F 4 HOH A 6 1306 28 HOH HOH . F 4 HOH A 7 1307 17 HOH HOH . F 4 HOH A 8 1308 18 HOH HOH . F 4 HOH A 9 1309 20 HOH HOH . F 4 HOH A 10 1310 15 HOH HOH . F 4 HOH A 11 1311 10 HOH HOH . F 4 HOH A 12 1312 14 HOH HOH . F 4 HOH A 13 1313 16 HOH HOH . F 4 HOH A 14 1314 33 HOH HOH . F 4 HOH A 15 1315 27 HOH HOH . F 4 HOH A 16 1316 24 HOH HOH . F 4 HOH A 17 1317 40 HOH HOH . F 4 HOH A 18 1318 36 HOH HOH . F 4 HOH A 19 1319 30 HOH HOH . F 4 HOH A 20 1320 11 HOH HOH . F 4 HOH A 21 1321 29 HOH HOH . F 4 HOH A 22 1322 8 HOH HOH . F 4 HOH A 23 1323 23 HOH HOH . F 4 HOH A 24 1324 39 HOH HOH . F 4 HOH A 25 1325 26 HOH HOH . F 4 HOH A 26 1326 34 HOH HOH . F 4 HOH A 27 1327 32 HOH HOH . F 4 HOH A 28 1328 13 HOH HOH . F 4 HOH A 29 1329 3 HOH HOH . F 4 HOH A 30 1330 37 HOH HOH . F 4 HOH A 31 1331 9 HOH HOH . F 4 HOH A 32 1332 5 HOH HOH . F 4 HOH A 33 1333 38 HOH HOH . F 4 HOH A 34 1334 1 HOH HOH . F 4 HOH A 35 1335 4 HOH HOH . F 4 HOH A 36 1336 6 HOH HOH . F 4 HOH A 37 1337 31 HOH HOH . F 4 HOH A 38 1338 22 HOH HOH . F 4 HOH A 39 1339 7 HOH HOH . F 4 HOH A 40 1340 12 HOH HOH . # 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 N N1 UDP . . . B 2 0.88 45.674 -12.047 1 46.69 ? N1 UDP 1201 A 1 HETATM 2 C C2 UDP . . . B 2 1.943 46.554 -11.881 1 51.77 ? C2 UDP 1201 A 1 HETATM 3 N N3 UDP . . . B 2 1.746 47.617 -11.099 1 57.35 ? N3 UDP 1201 A 1 HETATM 4 C C4 UDP . . . B 2 0.565 47.891 -10.509 1 50.38 ? C4 UDP 1201 A 1 HETATM 5 C C5 UDP . . . B 2 -0.518 47.038 -10.67 1 47.86 ? C5 UDP 1201 A 1 HETATM 6 C C6 UDP . . . B 2 -0.311 45.914 -11.481 1 54.05 ? C6 UDP 1201 A 1 HETATM 7 O O2 UDP . . . B 2 3.053 46.339 -12.429 1 57.03 ? O2 UDP 1201 A 1 HETATM 8 O O4 UDP . . . B 2 0.475 48.923 -9.819 1 44.59 ? O4 UDP 1201 A 1 HETATM 9 C C1' UDP . . . B 2 1.098 44.586 -12.933 1 45.78 ? C1' UDP 1201 A 1 HETATM 10 C C2' UDP . . . B 2 0.795 43.206 -12.489 1 47.31 ? C2' UDP 1201 A 1 HETATM 11 O O2' UDP . . . B 2 1.896 42.798 -11.694 1 49.51 ? O2' UDP 1201 A 1 HETATM 12 C C3' UDP . . . B 2 0.707 42.526 -13.851 1 48.77 ? C3' UDP 1201 A 1 HETATM 13 C C4' UDP . . . B 2 0.071 43.607 -14.725 1 48.46 ? C4' UDP 1201 A 1 HETATM 14 O O4' UDP . . . B 2 0.276 44.858 -14.064 1 47.68 ? O4' UDP 1201 A 1 HETATM 15 O O3' UDP . . . B 2 2.003 42.162 -14.322 1 51.43 ? O3' UDP 1201 A 1 HETATM 16 C C5' UDP . . . B 2 -1.437 43.423 -14.856 1 48.56 ? C5' UDP 1201 A 1 HETATM 17 O O5' UDP . . . B 2 -1.614 42.434 -15.839 1 52.99 ? O5' UDP 1201 A 1 HETATM 18 P PA UDP . . . B 2 -2.975 41.686 -16.095 1 44.94 ? PA UDP 1201 A 1 HETATM 19 O O1A UDP . . . B 2 -2.665 40.875 -17.323 1 46.79 ? O1A UDP 1201 A 1 HETATM 20 O O2A UDP . . . B 2 -3.919 42.818 -15.956 1 48.07 ? O2A UDP 1201 A 1 HETATM 21 O O3A UDP . . . B 2 -3.003 40.792 -14.797 1 49.83 ? O3A UDP 1201 A 1 HETATM 22 P PB UDP . . . B 2 -3.584 39.302 -14.652 1 49.23 ? PB UDP 1201 A 1 HETATM 23 O O1B UDP . . . B 2 -4.792 39.259 -15.528 1 51.81 ? O1B UDP 1201 A 1 HETATM 24 O O2B UDP . . . B 2 -2.565 38.301 -15.094 1 50.07 ? O2B UDP 1201 A 1 HETATM 25 O O3B UDP . . . B 2 -3.746 39.381 -13.131 1 48.93 ? O3B UDP 1201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #