data_5D4G # _model_server_result.job_id TuzjGRN0E34683ymAHY5nA _model_server_result.datetime_utc '2024-11-13 20:08:36' _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 5d4g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 5D4G # _exptl.entry_id 5D4G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 5D4G _cell.length_a 73.783 _cell.length_b 73.783 _cell.length_c 129.879 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D4G _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 D _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 NE2 HIS 41 A HIS 41 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc2 A OE2 GLU 61 A GLU 61 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc3 A OD2 ASP 89 A ASP 89 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.784 ? metalc ? metalc4 A OD1 ASP 89 A ASP 89 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.855 ? metalc ? metalc5 A OE2 GLU 100 A GLU 100 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc6 A O ILE 101 A ILE 101 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc7 B MN MN . A MN 201 1_555 D O2P U5P . A U5P 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc8 B MN MN . A MN 201 1_555 D O3P U5P . A U5P 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc9 C MN MN . A MN 202 1_555 D O3P U5P . A U5P 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc10 C MN MN . A MN 202 1_555 E O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc11 C MN MN . A MN 202 1_555 E O HOH . A HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc12 C MN MN . A MN 202 1_555 E O HOH . A HOH 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _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 N1 C2 U5P sing 358 n n N1 C6 U5P sing 359 n n N1 C1' U5P sing 360 n n C2 N3 U5P sing 361 n n C2 O2 U5P doub 362 n n N3 C4 U5P sing 363 n n N3 HN3 U5P sing 364 n n C4 C5 U5P sing 365 n n C4 O4 U5P doub 366 n n C5 C6 U5P doub 367 n n C5 H5 U5P sing 368 n n C6 H6 U5P sing 369 n n C1' C2' U5P sing 370 n n C1' O4' U5P sing 371 n n C1' H1' U5P sing 372 n n C2' O2' U5P sing 373 n n C2' C3' U5P sing 374 n n C2' H2' U5P sing 375 n n O2' HO2' U5P sing 376 n n C3' C4' U5P sing 377 n n C3' O3' U5P sing 378 n n C3' H3' U5P sing 379 n n C4' O4' U5P sing 380 n n C4' C5' U5P sing 381 n n C4' H4' U5P sing 382 n n O3' HO3' U5P sing 383 n n C5' O5' U5P sing 384 n n C5' "H5'1" U5P sing 385 n n C5' "H5'2" U5P sing 386 n n O5' P U5P sing 387 n n P O1P U5P doub 388 n n P O2P U5P sing 389 n n P O3P U5P sing 390 n n O2P HOP2 U5P sing 391 n n O3P HOP3 U5P sing 392 n n # _atom_sites.entry_id 5D4G _atom_sites.fract_transf_matrix[1][1] 0.013553 _atom_sites.fract_transf_matrix[1][2] 0.007825 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01565 _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] 0.007699 _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 MN A 1 201 201 MN MN . C 2 MN A 1 202 202 MN MN . D 3 U5P A 1 203 1 U5P U5P . E 4 HOH A 1 301 9 HOH HOH . E 4 HOH A 2 302 1 HOH HOH . E 4 HOH A 3 303 35 HOH HOH . E 4 HOH A 4 304 19 HOH HOH . E 4 HOH A 5 305 10 HOH HOH . E 4 HOH A 6 306 45 HOH HOH . E 4 HOH A 7 307 48 HOH HOH . E 4 HOH A 8 308 11 HOH HOH . E 4 HOH A 9 309 32 HOH HOH . E 4 HOH A 10 310 14 HOH HOH . E 4 HOH A 11 311 36 HOH HOH . E 4 HOH A 12 312 37 HOH HOH . E 4 HOH A 13 313 18 HOH HOH . E 4 HOH A 14 314 42 HOH HOH . E 4 HOH A 15 315 29 HOH HOH . E 4 HOH A 16 316 6 HOH HOH . E 4 HOH A 17 317 8 HOH HOH . E 4 HOH A 18 318 23 HOH HOH . E 4 HOH A 19 319 4 HOH HOH . E 4 HOH A 20 320 28 HOH HOH . E 4 HOH A 21 321 38 HOH HOH . E 4 HOH A 22 322 24 HOH HOH . E 4 HOH A 23 323 31 HOH HOH . E 4 HOH A 24 324 16 HOH HOH . E 4 HOH A 25 325 27 HOH HOH . E 4 HOH A 26 326 3 HOH HOH . E 4 HOH A 27 327 44 HOH HOH . E 4 HOH A 28 328 12 HOH HOH . E 4 HOH A 29 329 7 HOH HOH . E 4 HOH A 30 330 40 HOH HOH . E 4 HOH A 31 331 53 HOH HOH . E 4 HOH A 32 332 2 HOH HOH . E 4 HOH A 33 333 5 HOH HOH . E 4 HOH A 34 334 34 HOH HOH . E 4 HOH A 35 335 13 HOH HOH . E 4 HOH A 36 336 25 HOH HOH . E 4 HOH A 37 337 26 HOH HOH . E 4 HOH A 38 338 47 HOH HOH . E 4 HOH A 39 339 30 HOH HOH . E 4 HOH A 40 340 20 HOH HOH . E 4 HOH A 41 341 43 HOH HOH . E 4 HOH A 42 342 22 HOH HOH . E 4 HOH A 43 343 39 HOH HOH . E 4 HOH A 44 344 21 HOH HOH . E 4 HOH A 45 345 33 HOH HOH . E 4 HOH A 46 346 52 HOH HOH . E 4 HOH A 47 347 15 HOH HOH . E 4 HOH A 48 348 17 HOH HOH . E 4 HOH A 49 349 50 HOH HOH . E 4 HOH A 50 350 46 HOH HOH . E 4 HOH A 51 351 41 HOH HOH . E 4 HOH A 52 352 51 HOH HOH . E 4 HOH A 53 353 49 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 U5P . . . D 3 28.717 -18.383 -14.643 1 68.48 ? N1 U5P 203 A 1 HETATM 2 C C2 U5P . . . D 3 29.52 -19.456 -14.152 1 75.91 ? C2 U5P 203 A 1 HETATM 3 N N3 U5P . . . D 3 30.149 -20.266 -15.02 1 75.58 ? N3 U5P 203 A 1 HETATM 4 C C4 U5P . . . D 3 29.984 -20.066 -16.333 1 75.22 ? C4 U5P 203 A 1 HETATM 5 C C5 U5P . . . D 3 29.198 -19.042 -16.845 1 71.56 ? C5 U5P 203 A 1 HETATM 6 C C6 U5P . . . D 3 28.555 -18.192 -15.97 1 70.41 ? C6 U5P 203 A 1 HETATM 7 O O2 U5P . . . D 3 29.653 -19.657 -12.921 1 71.1 ? O2 U5P 203 A 1 HETATM 8 O O4 U5P . . . D 3 30.551 -20.834 -17.106 1 79.39 ? O4 U5P 203 A 1 HETATM 9 C C1' U5P . . . D 3 28.008 -17.568 -13.654 1 64.57 ? C1' U5P 203 A 1 HETATM 10 C C2' U5P . . . D 3 28.597 -16.205 -13.354 1 64.5 ? C2' U5P 203 A 1 HETATM 11 O O2' U5P . . . D 3 29.693 -16.438 -12.487 1 70.57 ? O2' U5P 203 A 1 HETATM 12 C C3' U5P . . . D 3 27.388 -15.445 -12.825 1 57.59 ? C3' U5P 203 A 1 HETATM 13 C C4' U5P . . . D 3 26.262 -16.049 -13.663 1 55.14 ? C4' U5P 203 A 1 HETATM 14 O O3' U5P . . . D 3 27.238 -15.795 -11.462 1 61.56 ? O3' U5P 203 A 1 HETATM 15 O O4' U5P . . . D 3 26.678 -17.33 -14.099 1 58.69 ? O4' U5P 203 A 1 HETATM 16 C C5' U5P . . . D 3 25.971 -15.29 -14.954 1 50.52 ? C5' U5P 203 A 1 HETATM 17 O O5' U5P . . . D 3 27.074 -15.274 -15.838 1 45.8 ? O5' U5P 203 A 1 HETATM 18 P P U5P . . . D 3 27.08 -14.143 -16.978 1 45.14 ? P U5P 203 A 1 HETATM 19 O O1P U5P . . . D 3 28.349 -14.628 -17.675 1 47.22 ? O1P U5P 203 A 1 HETATM 20 O O2P U5P . . . D 3 27.084 -12.864 -16.095 1 45.72 ? O2P U5P 203 A 1 HETATM 21 O O3P U5P . . . D 3 25.724 -14.091 -17.668 1 40.91 ? O3P U5P 203 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #