data_3ZF6 # _model_server_result.job_id JIrgl7hj0tCb9140StdILw _model_server_result.datetime_utc '2025-03-28 22:24:14' _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 3zf6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1172}' # _entry.id 3ZF6 # _exptl.entry_id 3ZF6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 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 3ZF6 _cell.length_a 87.46 _cell.length_b 87.46 _cell.length_c 87.46 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZF6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # 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' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 3 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 OD1 ASP 129 A ASP 95 1_555 B NI NI . A NI 1171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc2 A OD1 ASP 129 A ASP 95 9_555 B NI NI . A NI 1171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc3 A OD1 ASP 129 A ASP 95 5_555 B NI NI . A NI 1171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc4 B NI NI . A NI 1171 1_555 E O HOH . A HOH 2011 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc5 B NI NI . A NI 1171 1_555 E O HOH . A HOH 2011 9_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc6 B NI NI . A NI 1171 1_555 E O HOH . A HOH 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 358 n n N1 C6 UMP sing 359 n n N1 C1' UMP sing 360 n n C2 N3 UMP sing 361 n n C2 O2 UMP doub 362 n n N3 C4 UMP sing 363 n n N3 HN3 UMP sing 364 n n C4 C5 UMP sing 365 n n C4 O4 UMP doub 366 n n C5 C6 UMP doub 367 n n C5 H5 UMP sing 368 n n C6 H6 UMP sing 369 n n C1' C2' UMP sing 370 n n C1' O4' UMP sing 371 n n C1' H1' UMP sing 372 n n C2' C3' UMP sing 373 n n C2' H2' UMP sing 374 n n C2' "H2''" UMP sing 375 n n C3' C4' UMP sing 376 n n C3' O3' UMP sing 377 n n C3' H3' UMP sing 378 n n C4' O4' UMP sing 379 n n C4' C5' UMP sing 380 n n C4' H4' UMP sing 381 n n O3' HO3' UMP sing 382 n n C5' O5' UMP sing 383 n n C5' H5' UMP sing 384 n n C5' "H5''" UMP sing 385 n n O5' P UMP sing 386 n n P OP1 UMP doub 387 n n P OP2 UMP sing 388 n n P OP3 UMP sing 389 n n OP2 HOP2 UMP sing 390 n n OP3 HOP3 UMP sing 391 n n # _atom_sites.entry_id 3ZF6 _atom_sites.fract_transf_matrix[1][1] 0.011434 _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] 0.011434 _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] 0.011434 _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 NI A 1 1171 1171 NI NI . C 3 UMP A 1 1172 1172 UMP UMP . D 2 NI A 1 1173 1173 NI NI . E 4 HOH A 1 2001 2001 HOH HOH . E 4 HOH A 2 2002 2002 HOH HOH . E 4 HOH A 3 2003 2003 HOH HOH . E 4 HOH A 4 2004 2004 HOH HOH . E 4 HOH A 5 2005 2005 HOH HOH . E 4 HOH A 6 2006 2006 HOH HOH . E 4 HOH A 7 2007 2007 HOH HOH . E 4 HOH A 8 2008 2008 HOH HOH . E 4 HOH A 9 2009 2009 HOH HOH . E 4 HOH A 10 2010 2010 HOH HOH . E 4 HOH A 11 2011 2011 HOH HOH . E 4 HOH A 12 2012 2012 HOH HOH . E 4 HOH A 13 2013 2013 HOH HOH . E 4 HOH A 14 2014 2014 HOH HOH . E 4 HOH A 15 2015 2015 HOH HOH . E 4 HOH A 16 2016 2016 HOH HOH . E 4 HOH A 17 2017 2017 HOH HOH . E 4 HOH A 18 2018 2018 HOH HOH . E 4 HOH A 19 2019 2019 HOH HOH . E 4 HOH A 20 2020 2020 HOH HOH . E 4 HOH A 21 2021 2021 HOH HOH . E 4 HOH A 22 2022 2022 HOH HOH . E 4 HOH A 23 2023 2023 HOH HOH . E 4 HOH A 24 2024 2024 HOH HOH . E 4 HOH A 25 2025 2025 HOH HOH . E 4 HOH A 26 2026 2026 HOH HOH . E 4 HOH A 27 2027 2027 HOH HOH . E 4 HOH A 28 2028 2028 HOH HOH . E 4 HOH A 29 2029 2029 HOH HOH . E 4 HOH A 30 2030 2030 HOH HOH . E 4 HOH A 31 2031 2031 HOH HOH . E 4 HOH A 32 2032 2032 HOH HOH . E 4 HOH A 33 2033 2033 HOH HOH . E 4 HOH A 34 2034 2034 HOH HOH . E 4 HOH A 35 2035 2035 HOH HOH . E 4 HOH A 36 2036 2036 HOH HOH . E 4 HOH A 37 2037 2037 HOH HOH . E 4 HOH A 38 2038 2038 HOH HOH . E 4 HOH A 39 2039 2039 HOH HOH . E 4 HOH A 40 2040 2040 HOH HOH . E 4 HOH A 41 2041 2041 HOH HOH . E 4 HOH A 42 2042 2042 HOH HOH . E 4 HOH A 43 2043 2043 HOH HOH . E 4 HOH A 44 2044 2044 HOH HOH . E 4 HOH A 45 2045 2045 HOH HOH . E 4 HOH A 46 2046 2046 HOH HOH . E 4 HOH A 47 2047 2047 HOH HOH . E 4 HOH A 48 2048 2048 HOH HOH . E 4 HOH A 49 2049 2049 HOH HOH . E 4 HOH A 50 2050 2050 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 UMP . . . C 3 -11.017 5.091 6.325 1 56.05 ? N1 UMP 1172 A 1 HETATM 2 C C2 UMP . . . C 3 -10.844 6.351 5.695 1 55.43 ? C2 UMP 1172 A 1 HETATM 3 N N3 UMP . . . C 3 -9.61 6.825 5.463 1 55.13 ? N3 UMP 1172 A 1 HETATM 4 C C4 UMP . . . C 3 -8.52 6.127 5.817 1 54.78 ? C4 UMP 1172 A 1 HETATM 5 C C5 UMP . . . C 3 -8.656 4.887 6.437 1 55.11 ? C5 UMP 1172 A 1 HETATM 6 C C6 UMP . . . C 3 -9.931 4.382 6.683 1 55.61 ? C6 UMP 1172 A 1 HETATM 7 O O2 UMP . . . C 3 -11.833 7.035 5.351 1 55.61 ? O2 UMP 1172 A 1 HETATM 8 O O4 UMP . . . C 3 -7.382 6.591 5.589 1 53.38 ? O4 UMP 1172 A 1 HETATM 9 C C1' UMP . . . C 3 -12.372 4.571 6.578 1 55.97 ? C1' UMP 1172 A 1 HETATM 10 C C2' UMP . . . C 3 -12.7 3.445 5.601 1 56.29 ? C2' UMP 1172 A 1 HETATM 11 C C3' UMP . . . C 3 -12.875 2.206 6.457 1 56.45 ? C3' UMP 1172 A 1 HETATM 12 C C4' UMP . . . C 3 -13.041 2.724 7.877 1 56.33 ? C4' UMP 1172 A 1 HETATM 13 O O3' UMP . . . C 3 -14.028 1.467 6.049 1 57.81 ? O3' UMP 1172 A 1 HETATM 14 O O4' UMP . . . C 3 -12.485 4.042 7.904 1 56.04 ? O4' UMP 1172 A 1 HETATM 15 C C5' UMP . . . C 3 -12.373 1.826 8.915 1 55.63 ? C5' UMP 1172 A 1 HETATM 16 O O5' UMP . . . C 3 -10.966 1.729 8.691 1 55.02 ? O5' UMP 1172 A 1 HETATM 17 P P UMP . . . C 3 -10.1 0.566 9.395 1 54.98 ? P UMP 1172 A 1 HETATM 18 O OP1 UMP . . . C 3 -10.766 -0.721 8.971 1 55.38 ? OP1 UMP 1172 A 1 HETATM 19 O OP2 UMP . . . C 3 -8.712 0.755 8.833 1 55.13 ? OP2 UMP 1172 A 1 HETATM 20 O OP3 UMP . . . C 3 -10.213 0.857 10.871 1 54.93 ? OP3 UMP 1172 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 20 #