data_4FIY # _model_server_result.job_id b3bmPoEy_e-7Jc251Wxz8g _model_server_result.datetime_utc '2025-02-27 06:58:52' _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 4fiy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":701}' # _entry.id 4FIY # _exptl.entry_id 4FIY _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 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 90 _cell.entry_id 4FIY _cell.length_a 150.398 _cell.length_b 150.398 _cell.length_c 147.378 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4FIY _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 ? tetrameric 4 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,H 1 1,2,3,4 B,F,G,I 2 1,5,6,7 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_765 -x+2,-y+1,z -1 0 0 0 -1 0 0 0 1 300.796 150.398 0 3 'crystal symmetry operation' 3_645 -y+3/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 225.597 -75.199 0 4 'crystal symmetry operation' 4_565 y+1/2,-x+3/2,z 0 1 0 -1 0 0 0 0 1 75.199 225.597 0 5 'crystal symmetry operation' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 150.398 0 0 6 'crystal symmetry operation' 3_545 -y+1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 75.199 -75.199 0 7 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 75.199 75.199 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 F N 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 276 A ASP 256 1_555 D MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc2 A NE2 HIS 416 A HIS 396 1_555 D MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc3 C O1B UDP . A UDP 701 1_555 D MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc4 B OD1 ASP 276 B ASP 256 1_555 G MN MN . B MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc5 B OD2 ASP 278 B ASP 258 1_555 G MN MN . B MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc6 B NE2 HIS 416 B HIS 396 1_555 G MN MN . B MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? # _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 371 n n N1 C6 UDP sing 372 n n N1 C1' UDP sing 373 n n C2 N3 UDP sing 374 n n C2 O2 UDP doub 375 n n N3 C4 UDP sing 376 n n N3 HN3 UDP sing 377 n n C4 C5 UDP sing 378 n n C4 O4 UDP doub 379 n n C5 C6 UDP doub 380 n n C5 H5 UDP sing 381 n n C6 H6 UDP sing 382 n n C1' C2' UDP sing 383 n n C1' O4' UDP sing 384 n n C1' H1' UDP sing 385 n n C2' O2' UDP sing 386 n n C2' C3' UDP sing 387 n n C2' H2' UDP sing 388 n n O2' HO2' UDP sing 389 n n C3' C4' UDP sing 390 n n C3' O3' UDP sing 391 n n C3' H3' UDP sing 392 n n C4' O4' UDP sing 393 n n C4' C5' UDP sing 394 n n C4' H4' UDP sing 395 n n O3' HO3' UDP sing 396 n n C5' O5' UDP sing 397 n n C5' "H5'1" UDP sing 398 n n C5' "H5'2" UDP sing 399 n n O5' PA UDP sing 400 n n PA O1A UDP doub 401 n n PA O2A UDP sing 402 n n PA O3A UDP sing 403 n n O2A HOA2 UDP sing 404 n n O3A PB UDP sing 405 n n PB O1B UDP doub 406 n n PB O2B UDP sing 407 n n PB O3B UDP sing 408 n n O2B HOB2 UDP sing 409 n n O3B HOB3 UDP sing 410 n n # _atom_sites.entry_id 4FIY _atom_sites.fract_transf_matrix[1][1] 0.006649 _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] 0.006649 _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] 0.006785 _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 UDP A 1 701 1 UDP UDP . D 3 MN A 1 702 1 MN MN . E 4 GOL A 1 703 1 GOL GOL . F 2 UDP B 1 701 1 UDP UDP . G 3 MN B 1 702 2 MN MN . H 5 HOH A 1 801 1 HOH HOH . H 5 HOH A 2 802 2 HOH HOH . H 5 HOH A 3 803 3 HOH HOH . H 5 HOH A 4 804 4 HOH HOH . H 5 HOH A 5 805 5 HOH HOH . H 5 HOH A 6 806 6 HOH HOH . H 5 HOH A 7 807 7 HOH HOH . H 5 HOH A 8 808 8 HOH HOH . H 5 HOH A 9 809 9 HOH HOH . H 5 HOH A 10 810 10 HOH HOH . I 5 HOH B 1 801 11 HOH HOH . I 5 HOH B 2 802 12 HOH HOH . I 5 HOH B 3 803 13 HOH HOH . I 5 HOH B 4 804 14 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 . . . F 2 80.57 45.939 30.437 1 107.45 ? N1 UDP 701 B 1 HETATM 2 C C2 UDP . . . F 2 80.425 47.327 30.478 1 104.21 ? C2 UDP 701 B 1 HETATM 3 N N3 UDP . . . F 2 79.38 47.934 29.796 1 99.75 ? N3 UDP 701 B 1 HETATM 4 C C4 UDP . . . F 2 78.477 47.176 29.075 1 96.85 ? C4 UDP 701 B 1 HETATM 5 C C5 UDP . . . F 2 78.623 45.793 29.033 1 99.08 ? C5 UDP 701 B 1 HETATM 6 C C6 UDP . . . F 2 79.799 45.237 29.539 1 104.52 ? C6 UDP 701 B 1 HETATM 7 O O2 UDP . . . F 2 81.206 48.04 31.114 1 103.49 ? O2 UDP 701 B 1 HETATM 8 O O4 UDP . . . F 2 77.559 47.728 28.479 1 91.09 ? O4 UDP 701 B 1 HETATM 9 C C1' UDP . . . F 2 81.684 45.266 31.173 1 113.54 ? C1' UDP 701 B 1 HETATM 10 C C2' UDP . . . F 2 81.204 44.554 32.447 1 116.09 ? C2' UDP 701 B 1 HETATM 11 O O2' UDP . . . F 2 81.523 45.261 33.632 1 113.14 ? O2' UDP 701 B 1 HETATM 12 C C3' UDP . . . F 2 81.891 43.197 32.437 1 118.42 ? C3' UDP 701 B 1 HETATM 13 C C4' UDP . . . F 2 82.571 43.079 31.068 1 119.31 ? C4' UDP 701 B 1 HETATM 14 O O4' UDP . . . F 2 82.343 44.295 30.368 1 116.56 ? O4' UDP 701 B 1 HETATM 15 O O3' UDP . . . F 2 82.822 43.094 33.5 1 117.64 ? O3' UDP 701 B 1 HETATM 16 C C5' UDP . . . F 2 82.08 41.913 30.198 1 122.26 ? C5' UDP 701 B 1 HETATM 17 O O5' UDP . . . F 2 81.185 41.046 30.873 1 126.89 ? O5' UDP 701 B 1 HETATM 18 P PA UDP . . . F 2 79.584 41.095 30.64 1 128.21 ? PA UDP 701 B 1 HETATM 19 O O1A UDP . . . F 2 78.892 40.35 31.717 1 129.3 ? O1A UDP 701 B 1 HETATM 20 O O2A UDP . . . F 2 79.081 42.484 30.59 1 127.39 ? O2A UDP 701 B 1 HETATM 21 O O3A UDP . . . F 2 79.341 40.355 29.227 1 128.76 ? O3A UDP 701 B 1 HETATM 22 P PB UDP . . . F 2 79.676 38.796 28.982 1 129.44 ? PB UDP 701 B 1 HETATM 23 O O1B UDP . . . F 2 80.694 38.727 27.91 1 128.03 ? O1B UDP 701 B 1 HETATM 24 O O2B UDP . . . F 2 78.448 38.088 28.542 1 129.13 ? O2B UDP 701 B 1 HETATM 25 O O3B UDP . . . F 2 80.214 38.164 30.212 1 129.81 ? O3B UDP 701 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 162 _model_server_stats.query_time_ms 516 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #