data_2ZA3 # _model_server_result.job_id 0jFgmN3aLkSClWdSGLiqyQ _model_server_result.datetime_utc '2024-12-02 08:15:50' _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 2za3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":600}' # _entry.id 2ZA3 # _exptl.entry_id 2ZA3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 2ZA3 _cell.length_a 202.5 _cell.length_b 202.5 _cell.length_c 44.7 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZA3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _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 330 n n N1 C6 U5P sing 331 n n N1 C1' U5P sing 332 n n C2 N3 U5P sing 333 n n C2 O2 U5P doub 334 n n N3 C4 U5P sing 335 n n N3 HN3 U5P sing 336 n n C4 C5 U5P sing 337 n n C4 O4 U5P doub 338 n n C5 C6 U5P doub 339 n n C5 H5 U5P sing 340 n n C6 H6 U5P sing 341 n n C1' C2' U5P sing 342 n n C1' O4' U5P sing 343 n n C1' H1' U5P sing 344 n n C2' O2' U5P sing 345 n n C2' C3' U5P sing 346 n n C2' H2' U5P sing 347 n n O2' HO2' U5P sing 348 n n C3' C4' U5P sing 349 n n C3' O3' U5P sing 350 n n C3' H3' U5P sing 351 n n C4' O4' U5P sing 352 n n C4' C5' U5P sing 353 n n C4' H4' U5P sing 354 n n O3' HO3' U5P sing 355 n n C5' O5' U5P sing 356 n n C5' "H5'1" U5P sing 357 n n C5' "H5'2" U5P sing 358 n n O5' P U5P sing 359 n n P O1P U5P doub 360 n n P O2P U5P sing 361 n n P O3P U5P sing 362 n n O2P HOP2 U5P sing 363 n n O3P HOP3 U5P sing 364 n n # _atom_sites.entry_id 2ZA3 _atom_sites.fract_transf_matrix[1][1] 0.004938 _atom_sites.fract_transf_matrix[1][2] 0.002851 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005702 _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] 0.022371 _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 U5P A 1 500 500 U5P U5P . D 2 U5P B 1 600 600 U5P U5P . E 3 HOH A 1 501 1 HOH WAT . E 3 HOH A 2 502 5 HOH WAT . E 3 HOH A 3 503 7 HOH WAT . E 3 HOH A 4 504 8 HOH WAT . E 3 HOH A 5 505 9 HOH WAT . E 3 HOH A 6 506 11 HOH WAT . E 3 HOH A 7 507 13 HOH WAT . E 3 HOH A 8 508 16 HOH WAT . E 3 HOH A 9 509 20 HOH WAT . E 3 HOH A 10 510 21 HOH WAT . E 3 HOH A 11 511 23 HOH WAT . E 3 HOH A 12 512 27 HOH WAT . E 3 HOH A 13 513 28 HOH WAT . E 3 HOH A 14 514 29 HOH WAT . E 3 HOH A 15 515 39 HOH WAT . E 3 HOH A 16 516 43 HOH WAT . E 3 HOH A 17 517 44 HOH WAT . E 3 HOH A 18 518 45 HOH WAT . E 3 HOH A 19 519 46 HOH WAT . E 3 HOH A 20 520 52 HOH WAT . E 3 HOH A 21 521 53 HOH WAT . E 3 HOH A 22 522 56 HOH WAT . F 3 HOH B 1 601 2 HOH WAT . F 3 HOH B 2 602 3 HOH WAT . F 3 HOH B 3 603 4 HOH WAT . F 3 HOH B 4 604 15 HOH WAT . F 3 HOH B 5 605 17 HOH WAT . F 3 HOH B 6 606 19 HOH WAT . F 3 HOH B 7 607 24 HOH WAT . F 3 HOH B 8 608 25 HOH WAT . F 3 HOH B 9 609 31 HOH WAT . F 3 HOH B 10 610 32 HOH WAT . F 3 HOH B 11 611 33 HOH WAT . F 3 HOH B 12 612 34 HOH WAT . F 3 HOH B 13 613 35 HOH WAT . F 3 HOH B 14 614 36 HOH WAT . F 3 HOH B 15 615 37 HOH WAT . F 3 HOH B 16 616 38 HOH WAT . F 3 HOH B 17 617 40 HOH WAT . F 3 HOH B 18 618 41 HOH WAT . F 3 HOH B 19 619 42 HOH WAT . F 3 HOH B 20 620 47 HOH WAT . F 3 HOH B 21 621 49 HOH WAT . F 3 HOH B 22 622 50 HOH WAT . F 3 HOH B 23 623 51 HOH WAT . F 3 HOH B 24 624 54 HOH WAT . F 3 HOH B 25 625 55 HOH WAT . # 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 2 -42.765 -3.37 -22.531 1 53.49 ? N1 U5P 600 B 1 HETATM 2 C C2 U5P . . . D 2 -43.534 -3.652 -23.643 1 58.51 ? C2 U5P 600 B 1 HETATM 3 N N3 U5P . . . D 2 -44.787 -4.167 -23.48 1 48.09 ? N3 U5P 600 B 1 HETATM 4 C C4 U5P . . . D 2 -45.295 -4.404 -22.231 1 49.27 ? C4 U5P 600 B 1 HETATM 5 C C5 U5P . . . D 2 -44.512 -4.116 -21.077 1 39.27 ? C5 U5P 600 B 1 HETATM 6 C C6 U5P . . . D 2 -43.263 -3.603 -21.255 1 51.64 ? C6 U5P 600 B 1 HETATM 7 O O2 U5P . . . D 2 -43.109 -3.451 -24.777 1 48.6 ? O2 U5P 600 B 1 HETATM 8 O O4 U5P . . . D 2 -46.414 -4.863 -22.102 1 63.64 ? O4 U5P 600 B 1 HETATM 9 C C1' U5P . . . D 2 -41.404 -2.819 -22.635 1 46.44 ? C1' U5P 600 B 1 HETATM 10 C C2' U5P . . . D 2 -40.402 -3.876 -23.176 1 48.26 ? C2' U5P 600 B 1 HETATM 11 O O2' U5P . . . D 2 -39.792 -4.554 -22.109 1 74.89 ? O2' U5P 600 B 1 HETATM 12 C C3' U5P . . . D 2 -39.438 -3.06 -24.012 1 48.57 ? C3' U5P 600 B 1 HETATM 13 C C4' U5P . . . D 2 -39.945 -1.619 -24.048 1 47.2 ? C4' U5P 600 B 1 HETATM 14 O O3' U5P . . . D 2 -38.12 -3.112 -23.457 1 40 ? O3' U5P 600 B 1 HETATM 15 O O4' U5P . . . D 2 -41.309 -1.661 -23.51 1 44.47 ? O4' U5P 600 B 1 HETATM 16 C C5' U5P . . . D 2 -39.94 -1.246 -25.536 1 53.64 ? C5' U5P 600 B 1 HETATM 17 O O5' U5P . . . D 2 -40.382 0.071 -25.784 1 52.31 ? O5' U5P 600 B 1 HETATM 18 P P U5P . . . D 2 -40.313 0.297 -27.394 1 56.41 ? P U5P 600 B 1 HETATM 19 O O1P U5P . . . D 2 -41.206 -0.676 -28.06 1 46.36 ? O1P U5P 600 B 1 HETATM 20 O O2P U5P . . . D 2 -40.804 1.806 -27.701 1 37.46 ? O2P U5P 600 B 1 HETATM 21 O O3P U5P . . . D 2 -38.822 0.088 -27.948 1 43.54 ? O3P U5P 600 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 1265 _model_server_stats.encode_time_ms 52 _model_server_stats.element_count 21 #