data_1XZ8 # _model_server_result.job_id KMuDdBiLSRENbWhsN0McaA _model_server_result.datetime_utc '2025-08-31 22:47:43' _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 1xz8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":400}' # _entry.id 1XZ8 # _exptl.entry_id 1XZ8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 5 _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 1XZ8 _cell.length_a 128.54 _cell.length_b 128.54 _cell.length_c 128.76 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XZ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F,G,H,I _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 5 _struct_asym.id G _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 OD2 ASP 104 A ASP 104 1_555 C MG MG . A MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc2 A OD1 ASP 105 A ASP 105 1_555 C MG MG . A MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc3 C MG MG . A MG 180 1_555 E O1P 3GP . A 3GP 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc4 C MG MG . A MG 180 1_555 H O HOH . A HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc5 C MG MG . A MG 180 1_555 H O HOH . A HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc6 C MG MG . A MG 180 1_555 H O HOH . A HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc7 B OD2 ASP 104 B ASP 104 1_555 F MG MG . B MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc8 B OD1 ASP 104 B ASP 104 1_555 F MG MG . B MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc9 B OD1 ASP 105 B ASP 105 1_555 F MG MG . B MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc10 F MG MG . B MG 180 1_555 G O3' U5P . B U5P 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc11 F MG MG . B MG 180 1_555 I O HOH . B HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.748 ? metalc ? metalc12 F MG MG . B MG 180 1_555 I O HOH . B HOH 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? # _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 410 n n N1 C6 U5P sing 411 n n N1 C1' U5P sing 412 n n C2 N3 U5P sing 413 n n C2 O2 U5P doub 414 n n N3 C4 U5P sing 415 n n N3 HN3 U5P sing 416 n n C4 C5 U5P sing 417 n n C4 O4 U5P doub 418 n n C5 C6 U5P doub 419 n n C5 H5 U5P sing 420 n n C6 H6 U5P sing 421 n n C1' C2' U5P sing 422 n n C1' O4' U5P sing 423 n n C1' H1' U5P sing 424 n n C2' O2' U5P sing 425 n n C2' C3' U5P sing 426 n n C2' H2' U5P sing 427 n n O2' HO2' U5P sing 428 n n C3' C4' U5P sing 429 n n C3' O3' U5P sing 430 n n C3' H3' U5P sing 431 n n C4' O4' U5P sing 432 n n C4' C5' U5P sing 433 n n C4' H4' U5P sing 434 n n O3' HO3' U5P sing 435 n n C5' O5' U5P sing 436 n n C5' "H5'1" U5P sing 437 n n C5' "H5'2" U5P sing 438 n n O5' P U5P sing 439 n n P O1P U5P doub 440 n n P O2P U5P sing 441 n n P O3P U5P sing 442 n n O2P HOP2 U5P sing 443 n n O3P HOP3 U5P sing 444 n n # _atom_sites.entry_id 1XZ8 _atom_sites.fract_transf_matrix[1][1] 0.00778 _atom_sites.fract_transf_matrix[1][2] 0.004492 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008983 _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] 0.007766 _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 C 2 MG A 1 180 100 MG MG . D 3 5GP A 1 200 200 5GP 5GP . E 4 3GP A 1 300 300 3GP 3GP . F 2 MG B 1 180 101 MG MG . G 5 U5P B 1 400 400 U5P U5P . H 6 HOH A 1 301 5 HOH HOH . H 6 HOH A 2 302 6 HOH HOH . H 6 HOH A 3 303 7 HOH HOH . H 6 HOH A 4 304 8 HOH HOH . H 6 HOH A 5 305 10 HOH HOH . H 6 HOH A 6 306 12 HOH HOH . H 6 HOH A 7 307 14 HOH HOH . H 6 HOH A 8 308 17 HOH HOH . H 6 HOH A 9 309 19 HOH HOH . H 6 HOH A 10 310 20 HOH HOH . H 6 HOH A 11 311 22 HOH HOH . H 6 HOH A 12 312 23 HOH HOH . H 6 HOH A 13 313 24 HOH HOH . H 6 HOH A 14 314 30 HOH HOH . H 6 HOH A 15 315 32 HOH HOH . H 6 HOH A 16 316 34 HOH HOH . H 6 HOH A 17 317 35 HOH HOH . H 6 HOH A 18 318 37 HOH HOH . H 6 HOH A 19 319 39 HOH HOH . H 6 HOH A 20 320 41 HOH HOH . H 6 HOH A 21 321 45 HOH HOH . H 6 HOH A 22 322 46 HOH HOH . H 6 HOH A 23 323 47 HOH HOH . H 6 HOH A 24 324 48 HOH HOH . H 6 HOH A 25 325 51 HOH HOH . H 6 HOH A 26 326 52 HOH HOH . H 6 HOH A 27 327 53 HOH HOH . H 6 HOH A 28 328 54 HOH HOH . I 6 HOH B 1 401 1 HOH HOH . I 6 HOH B 2 402 2 HOH HOH . I 6 HOH B 3 403 3 HOH HOH . I 6 HOH B 4 404 4 HOH HOH . I 6 HOH B 5 405 9 HOH HOH . I 6 HOH B 6 406 11 HOH HOH . I 6 HOH B 7 407 13 HOH HOH . I 6 HOH B 8 408 15 HOH HOH . I 6 HOH B 9 409 16 HOH HOH . I 6 HOH B 10 410 18 HOH HOH . I 6 HOH B 11 411 21 HOH HOH . I 6 HOH B 12 412 25 HOH HOH . I 6 HOH B 13 413 26 HOH HOH . I 6 HOH B 14 414 27 HOH HOH . I 6 HOH B 15 415 28 HOH HOH . I 6 HOH B 16 416 31 HOH HOH . I 6 HOH B 17 417 33 HOH HOH . I 6 HOH B 18 418 36 HOH HOH . I 6 HOH B 19 419 38 HOH HOH . I 6 HOH B 20 420 40 HOH HOH . I 6 HOH B 21 421 42 HOH HOH . I 6 HOH B 22 422 43 HOH HOH . I 6 HOH B 23 423 44 HOH HOH . I 6 HOH B 24 424 49 HOH HOH . I 6 HOH B 25 425 50 HOH HOH . I 6 HOH B 26 426 55 HOH HOH . I 6 HOH B 27 427 56 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 . . . G 5 20.255 29.718 5.136 1 78.65 ? N1 U5P 400 B 1 HETATM 2 C C2 U5P . . . G 5 20.542 31.114 5.059 1 79.6 ? C2 U5P 400 B 1 HETATM 3 N N3 U5P . . . G 5 20.535 31.764 6.292 1 79.58 ? N3 U5P 400 B 1 HETATM 4 C C4 U5P . . . G 5 20.281 31.202 7.579 1 78.84 ? C4 U5P 400 B 1 HETATM 5 C C5 U5P . . . G 5 20.001 29.797 7.579 1 78.15 ? C5 U5P 400 B 1 HETATM 6 C C6 U5P . . . G 5 19.995 29.133 6.438 1 78.16 ? C6 U5P 400 B 1 HETATM 7 O O2 U5P . . . G 5 20.77 31.666 3.997 1 81.09 ? O2 U5P 400 B 1 HETATM 8 O O4 U5P . . . G 5 20.318 31.936 8.541 1 78.77 ? O4 U5P 400 B 1 HETATM 9 C C1' U5P . . . G 5 20.222 28.847 3.857 1 77.66 ? C1' U5P 400 B 1 HETATM 10 C C2' U5P . . . G 5 21.614 28.827 3.174 1 77.15 ? C2' U5P 400 B 1 HETATM 11 O O2' U5P . . . G 5 21.562 28.905 1.7 1 75.69 ? O2' U5P 400 B 1 HETATM 12 C C3' U5P . . . G 5 22.254 27.583 3.74 1 76.29 ? C3' U5P 400 B 1 HETATM 13 C C4' U5P . . . G 5 21.037 26.632 3.903 1 74.66 ? C4' U5P 400 B 1 HETATM 14 O O3' U5P . . . G 5 23.316 27.088 2.863 1 74.98 ? O3' U5P 400 B 1 HETATM 15 O O4' U5P . . . G 5 19.925 27.533 4.231 1 76.06 ? O4' U5P 400 B 1 HETATM 16 C C5' U5P . . . G 5 21.119 25.725 5.126 1 72.23 ? C5' U5P 400 B 1 HETATM 17 O O5' U5P . . . G 5 20.28 24.558 5.017 1 68.57 ? O5' U5P 400 B 1 HETATM 18 P P U5P . . . G 5 19.757 23.755 6.305 1 63.55 ? P U5P 400 B 1 HETATM 19 O O1P U5P . . . G 5 20.776 23.194 7.243 1 62.41 ? O1P U5P 400 B 1 HETATM 20 O O2P U5P . . . G 5 18.933 22.59 5.896 1 63.72 ? O2P U5P 400 B 1 HETATM 21 O O3P U5P . . . G 5 18.634 24.825 6.918 1 60.77 ? O3P U5P 400 B 1 # _model_server_stats.io_time_ms 4 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 432 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #