data_2J0B # _model_server_result.job_id i7OBgbJuRkqPpThfmdlwRA _model_server_result.datetime_utc '2024-10-19 23:41:44' _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 2j0b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1322}' # _entry.id 2J0B # _exptl.entry_id 2J0B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 2J0B _cell.length_a 161.76 _cell.length_b 40.97 _cell.length_c 38.37 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2J0B _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PQS _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,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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 disulf ? disulf1 A SG CYS 69 A CYS 110 1_555 A SG CYS 80 A CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 98 A CYS 139 1_555 A SG CYS 161 A CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? disulf ? disulf3 A SG CYS 265 A CYS 306 1_555 A SG CYS 274 A CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc1 C K K . A K 1320 1_555 A O ALA 77 A ALA 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc2 C K K . A K 1320 1_555 A O LEU 185 A LEU 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? metalc ? metalc3 C K K . A K 1320 1_555 A O LEU 188 A LEU 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? metalc ? metalc4 C K K . A K 1320 1_555 A OG1 THR 193 A THR 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc5 C K K . A K 1320 1_555 F O HOH . A HOH 2052 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc6 D MN MN . A MN 1321 1_555 E O1A UDP . A UDP 1322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc7 D MN MN . A MN 1321 1_555 E O3B UDP . A UDP 1322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc8 D MN MN . A MN 1321 1_555 F O HOH . A HOH 2084 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc9 D MN MN . A MN 1321 1_555 F O HOH . A HOH 2083 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc10 D MN MN . A MN 1321 1_555 A OD2 ASP 103 A ASP 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc11 D MN MN . A MN 1321 1_555 A NE2 HIS 215 A HIS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? # _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 ? # _atom_sites.entry_id 2J0B _atom_sites.fract_transf_matrix[1][1] 0.006182 _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] 0.024408 _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] 0.026062 _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 SO4 A 1 1319 1319 SO4 SO4 . C 3 K A 1 1320 1320 K K . D 4 MN A 1 1321 1321 MN MN . E 5 UDP A 1 1322 1322 UDP UDP . F 6 HOH A 1 2001 2001 HOH HOH . F 6 HOH A 2 2002 2002 HOH HOH . F 6 HOH A 3 2003 2003 HOH HOH . F 6 HOH A 4 2004 2004 HOH HOH . F 6 HOH A 5 2005 2005 HOH HOH . F 6 HOH A 6 2006 2006 HOH HOH . F 6 HOH A 7 2007 2007 HOH HOH . F 6 HOH A 8 2008 2008 HOH HOH . F 6 HOH A 9 2009 2009 HOH HOH . F 6 HOH A 10 2010 2010 HOH HOH . F 6 HOH A 11 2011 2011 HOH HOH . F 6 HOH A 12 2012 2012 HOH HOH . F 6 HOH A 13 2013 2013 HOH HOH . F 6 HOH A 14 2014 2014 HOH HOH . F 6 HOH A 15 2015 2015 HOH HOH . F 6 HOH A 16 2016 2016 HOH HOH . F 6 HOH A 17 2017 2017 HOH HOH . F 6 HOH A 18 2018 2018 HOH HOH . F 6 HOH A 19 2019 2019 HOH HOH . F 6 HOH A 20 2020 2020 HOH HOH . F 6 HOH A 21 2021 2021 HOH HOH . F 6 HOH A 22 2022 2022 HOH HOH . F 6 HOH A 23 2023 2023 HOH HOH . F 6 HOH A 24 2024 2024 HOH HOH . F 6 HOH A 25 2025 2025 HOH HOH . F 6 HOH A 26 2026 2026 HOH HOH . F 6 HOH A 27 2027 2027 HOH HOH . F 6 HOH A 28 2028 2028 HOH HOH . F 6 HOH A 29 2029 2029 HOH HOH . F 6 HOH A 30 2030 2030 HOH HOH . F 6 HOH A 31 2031 2031 HOH HOH . F 6 HOH A 32 2032 2032 HOH HOH . F 6 HOH A 33 2033 2033 HOH HOH . F 6 HOH A 34 2034 2034 HOH HOH . F 6 HOH A 35 2035 2035 HOH HOH . F 6 HOH A 36 2036 2036 HOH HOH . F 6 HOH A 37 2037 2037 HOH HOH . F 6 HOH A 38 2038 2038 HOH HOH . F 6 HOH A 39 2039 2039 HOH HOH . F 6 HOH A 40 2040 2040 HOH HOH . F 6 HOH A 41 2041 2041 HOH HOH . F 6 HOH A 42 2042 2042 HOH HOH . F 6 HOH A 43 2043 2043 HOH HOH . F 6 HOH A 44 2044 2044 HOH HOH . F 6 HOH A 45 2045 2045 HOH HOH . F 6 HOH A 46 2046 2046 HOH HOH . F 6 HOH A 47 2047 2047 HOH HOH . F 6 HOH A 48 2048 2048 HOH HOH . F 6 HOH A 49 2049 2049 HOH HOH . F 6 HOH A 50 2050 2050 HOH HOH . F 6 HOH A 51 2051 2051 HOH HOH . F 6 HOH A 52 2052 2052 HOH HOH . F 6 HOH A 53 2053 2053 HOH HOH . F 6 HOH A 54 2054 2054 HOH HOH . F 6 HOH A 55 2055 2055 HOH HOH . F 6 HOH A 56 2056 2056 HOH HOH . F 6 HOH A 57 2057 2057 HOH HOH . F 6 HOH A 58 2058 2058 HOH HOH . F 6 HOH A 59 2059 2059 HOH HOH . F 6 HOH A 60 2060 2060 HOH HOH . F 6 HOH A 61 2061 2061 HOH HOH . F 6 HOH A 62 2062 2062 HOH HOH . F 6 HOH A 63 2063 2063 HOH HOH . F 6 HOH A 64 2064 2064 HOH HOH . F 6 HOH A 65 2065 2065 HOH HOH . F 6 HOH A 66 2066 2066 HOH HOH . F 6 HOH A 67 2067 2067 HOH HOH . F 6 HOH A 68 2068 2068 HOH HOH . F 6 HOH A 69 2069 2069 HOH HOH . F 6 HOH A 70 2070 2070 HOH HOH . F 6 HOH A 71 2071 2071 HOH HOH . F 6 HOH A 72 2072 2072 HOH HOH . F 6 HOH A 73 2073 2073 HOH HOH . F 6 HOH A 74 2074 2074 HOH HOH . F 6 HOH A 75 2075 2075 HOH HOH . F 6 HOH A 76 2076 2076 HOH HOH . F 6 HOH A 77 2077 2077 HOH HOH . F 6 HOH A 78 2078 2078 HOH HOH . F 6 HOH A 79 2079 2079 HOH HOH . F 6 HOH A 80 2080 2080 HOH HOH . F 6 HOH A 81 2081 2081 HOH HOH . F 6 HOH A 82 2082 2082 HOH HOH . F 6 HOH A 83 2083 2083 HOH HOH . F 6 HOH A 84 2084 2084 HOH HOH . F 6 HOH A 85 2085 2085 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 . . . E 5 24.646 -7.597 43.92 1 38.42 ? N1 UDP 1322 A 1 HETATM 2 C C2 UDP . . . E 5 23.695 -7.259 44.887 1 40.8 ? C2 UDP 1322 A 1 HETATM 3 N N3 UDP . . . E 5 23.644 -7.986 46.058 1 42.26 ? N3 UDP 1322 A 1 HETATM 4 C C4 UDP . . . E 5 24.515 -9.048 46.251 1 42.73 ? C4 UDP 1322 A 1 HETATM 5 C C5 UDP . . . E 5 25.464 -9.395 45.277 1 41.5 ? C5 UDP 1322 A 1 HETATM 6 C C6 UDP . . . E 5 25.469 -8.699 44.077 1 40.38 ? C6 UDP 1322 A 1 HETATM 7 O O2 UDP . . . E 5 22.91 -6.32 44.704 1 39.09 ? O2 UDP 1322 A 1 HETATM 8 O O4 UDP . . . E 5 24.46 -9.668 47.313 1 44.94 ? O4 UDP 1322 A 1 HETATM 9 C C1' UDP . . . E 5 24.647 -6.811 42.68 1 34.19 ? C1' UDP 1322 A 1 HETATM 10 C C2' UDP . . . E 5 25.996 -6.233 42.254 1 32.8 ? C2' UDP 1322 A 1 HETATM 11 O O2' UDP . . . E 5 26.234 -4.993 42.838 1 30.91 ? O2' UDP 1322 A 1 HETATM 12 C C3' UDP . . . E 5 25.861 -6.16 40.734 1 29.78 ? C3' UDP 1322 A 1 HETATM 13 C C4' UDP . . . E 5 24.976 -7.368 40.444 1 32.84 ? C4' UDP 1322 A 1 HETATM 14 O O4' UDP . . . E 5 24.26 -7.687 41.655 1 31.09 ? O4' UDP 1322 A 1 HETATM 15 O O3' UDP . . . E 5 25.223 -4.993 40.274 1 26.94 ? O3' UDP 1322 A 1 HETATM 16 C C5' UDP . . . E 5 25.824 -8.56 39.97 1 32.44 ? C5' UDP 1322 A 1 HETATM 17 O O5' UDP . . . E 5 26.74 -8.859 41.002 1 33.05 ? O5' UDP 1322 A 1 HETATM 18 P PA UDP . . . E 5 28.07 -9.699 40.66 1 33.29 ? PA UDP 1322 A 1 HETATM 19 O O1A UDP . . . E 5 28.72 -9.08 39.506 1 33.7 ? O1A UDP 1322 A 1 HETATM 20 O O2A UDP . . . E 5 28.98 -9.962 41.809 1 32.64 ? O2A UDP 1322 A 1 HETATM 21 O O3A UDP . . . E 5 27.345 -11.116 40.292 1 39.9 ? O3A UDP 1322 A 1 HETATM 22 P PB UDP . . . E 5 27.484 -11.977 38.933 1 39.21 ? PB UDP 1322 A 1 HETATM 23 O O1B UDP . . . E 5 26.146 -12.549 38.659 1 41.13 ? O1B UDP 1322 A 1 HETATM 24 O O2B UDP . . . E 5 28.454 -13.044 39.282 1 42.69 ? O2B UDP 1322 A 1 HETATM 25 O O3B UDP . . . E 5 27.88 -11.153 37.782 1 38.85 ? O3B UDP 1322 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #