data_5DEB # _model_server_result.job_id veo5D_x2UtxCXZ_nF1HylQ _model_server_result.datetime_utc '2024-11-15 02:21:49' _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 5deb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 5DEB # _exptl.entry_id 5DEB _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 90 _cell.entry_id 5DEB _cell.length_a 90.057 _cell.length_b 90.057 _cell.length_c 134.337 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DEB _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 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 61 A HIS 41 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc2 A OD2 ASP 109 A ASP 89 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc3 A OD1 ASP 109 A ASP 89 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc4 A OD1 ASP 120 A ASP 100 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc5 A O ILE 121 A ILE 101 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc6 B MN MN . A MN 201 1_555 D O2P U5P . A U5P 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc7 B MN MN . A MN 201 1_555 D O1P U5P . A U5P 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc8 C MN MN . A MN 202 1_555 D O1P U5P . A U5P 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? # _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 5DEB _atom_sites.fract_transf_matrix[1][1] 0.011104 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011104 _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] 0.007444 _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 1 MN MN . C 2 MN A 1 202 2 MN MN . D 3 U5P A 1 203 1 U5P U5P . E 4 HOH A 1 301 15 HOH HOH . E 4 HOH A 2 302 18 HOH HOH . E 4 HOH A 3 303 7 HOH HOH . E 4 HOH A 4 304 8 HOH HOH . E 4 HOH A 5 305 21 HOH HOH . E 4 HOH A 6 306 5 HOH HOH . E 4 HOH A 7 307 10 HOH HOH . E 4 HOH A 8 308 16 HOH HOH . E 4 HOH A 9 309 6 HOH HOH . E 4 HOH A 10 310 17 HOH HOH . E 4 HOH A 11 311 4 HOH HOH . E 4 HOH A 12 312 20 HOH HOH . E 4 HOH A 13 313 14 HOH HOH . E 4 HOH A 14 314 13 HOH HOH . E 4 HOH A 15 315 19 HOH HOH . E 4 HOH A 16 316 1 HOH HOH . E 4 HOH A 17 317 12 HOH HOH . E 4 HOH A 18 318 22 HOH HOH . E 4 HOH A 19 319 11 HOH HOH . E 4 HOH A 20 320 3 HOH HOH . E 4 HOH A 21 321 2 HOH HOH . E 4 HOH A 22 322 9 HOH HOH . E 4 HOH A 23 323 23 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 3 129.345 103.278 282.599 1 103.82 ? N1 U5P 203 A 1 HETATM 2 C C2 U5P . . . D 3 129.378 102.186 281.68 1 105.63 ? C2 U5P 203 A 1 HETATM 3 N N3 U5P . . . D 3 130.492 101.427 281.538 1 112.73 ? N3 U5P 203 A 1 HETATM 4 C C4 U5P . . . D 3 131.605 101.69 282.267 1 117.76 ? C4 U5P 203 A 1 HETATM 5 C C5 U5P . . . D 3 131.617 102.758 283.171 1 113.29 ? C5 U5P 203 A 1 HETATM 6 C C6 U5P . . . D 3 130.472 103.549 283.316 1 107.37 ? C6 U5P 203 A 1 HETATM 7 O O2 U5P . . . D 3 128.369 101.934 280.991 1 100.67 ? O2 U5P 203 A 1 HETATM 8 O O4 U5P . . . D 3 132.633 100.985 282.141 1 126.57 ? O4 U5P 203 A 1 HETATM 9 C C1' U5P . . . D 3 128.113 104.118 282.682 1 101.56 ? C1' U5P 203 A 1 HETATM 10 C C2' U5P . . . D 3 127.063 103.715 283.73 1 96.52 ? C2' U5P 203 A 1 HETATM 11 O O2' U5P . . . D 3 126.08 102.867 283.129 1 94.54 ? O2' U5P 203 A 1 HETATM 12 C C3' U5P . . . D 3 126.511 105.054 284.227 1 97.45 ? C3' U5P 203 A 1 HETATM 13 C C4' U5P . . . D 3 127.583 106.092 283.851 1 98.3 ? C4' U5P 203 A 1 HETATM 14 O O3' U5P . . . D 3 125.268 105.446 283.637 1 94.57 ? O3' U5P 203 A 1 HETATM 15 O O4' U5P . . . D 3 128.457 105.517 282.891 1 102.3 ? O4' U5P 203 A 1 HETATM 16 C C5' U5P . . . D 3 128.467 106.475 285.015 1 100.39 ? C5' U5P 203 A 1 HETATM 17 O O5' U5P . . . D 3 129.019 105.387 285.754 1 103.95 ? O5' U5P 203 A 1 HETATM 18 P P U5P . . . D 3 129.554 105.615 287.274 1 115.39 ? P U5P 203 A 1 HETATM 19 O O1P U5P . . . D 3 130.745 106.541 287.138 1 118.59 ? O1P U5P 203 A 1 HETATM 20 O O2P U5P . . . D 3 128.385 106.164 288.096 1 103.11 ? O2P U5P 203 A 1 HETATM 21 O O3P U5P . . . D 3 130.021 104.233 287.668 1 119.68 ? O3P U5P 203 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #