data_1PN3 # _model_server_result.job_id K9sUTr53-zbiWiI3FG21kQ _model_server_result.datetime_utc '2024-11-23 06:50:03' _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 1pn3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":406}' # _entry.id 1PN3 # _exptl.entry_id 1PN3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-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 120 _cell.entry_id 1PN3 _cell.length_a 152.5 _cell.length_b 152.5 _cell.length_c 98.74 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PN3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_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,E,F,H,J 1 1 B,D,G,I,K 2 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 3 _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 covale ? covale1 C C MLU 1 C MLU 1 1_555 C N OMZ 2 C OMZ 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.362 ? covale ? covale2 C C OMZ 2 C OMZ 2 1_555 C N ASN 3 C ASN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.367 ? covale ? covale3 C OH OMZ 2 C OMZ 2 1_555 C C5 GHP 4 C GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale4 C C ASN 3 C ASN 3 1_555 C N GHP 4 C GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale5 C C GHP 4 C GHP 4 1_555 C N GHP 5 C GHP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.364 ? covale ? covale6 C C3 GHP 4 C GHP 4 1_555 C OCZ OMY 6 C OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 C O4 GHP 4 C GHP 4 1_555 F C1 BGC . C BGC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale8 C C GHP 5 C GHP 5 1_555 C N OMY 6 C OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? covale ? covale9 C C3 GHP 5 C GHP 5 1_555 C CG1 3FG 7 C 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.506 ? covale ? covale10 C C OMY 6 C OMY 6 1_555 C N 3FG 7 C 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale11 D C MLU 1 D MLU 1 1_555 D N OMZ 2 D OMZ 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale12 D C OMZ 2 D OMZ 2 1_555 D N ASN 3 D ASN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.36 ? covale ? covale13 D OH OMZ 2 D OMZ 2 1_555 D C5 GHP 4 D GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale14 D C ASN 3 D ASN 3 1_555 D N GHP 4 D GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale15 D C GHP 4 D GHP 4 1_555 D N GHP 5 D GHP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale16 D C3 GHP 4 D GHP 4 1_555 D OCZ OMY 6 D OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale17 D O4 GHP 4 D GHP 4 1_555 G C1 BGC . D BGC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale18 D C GHP 5 D GHP 5 1_555 D N OMY 6 D OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale19 D C3 GHP 5 D GHP 5 1_555 D CG1 3FG 7 D 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.532 ? covale ? covale20 D C OMY 6 D OMY 6 1_555 D N 3FG 7 D 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1PN3 _atom_sites.fract_transf_matrix[1][1] 0.006557 _atom_sites.fract_transf_matrix[1][2] 0.003786 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007572 _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] 0.010128 _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 E 3 TYD A 1 406 406 TYD TYD . F 4 BGC C 1 8 8 BGC BGC . G 4 BGC D 1 8 8 BGC BGC . H 5 HOH A 1 2001 2001 HOH HOH . H 5 HOH A 2 2002 2002 HOH HOH . H 5 HOH A 3 2003 2003 HOH HOH . H 5 HOH A 4 2004 2004 HOH HOH . H 5 HOH A 5 2005 2005 HOH HOH . H 5 HOH A 6 2006 2006 HOH HOH . H 5 HOH A 7 2007 2007 HOH HOH . H 5 HOH A 8 2008 2008 HOH HOH . H 5 HOH A 9 2009 2009 HOH HOH . H 5 HOH A 10 2010 2010 HOH HOH . H 5 HOH A 11 2011 2011 HOH HOH . H 5 HOH A 12 2012 2012 HOH HOH . H 5 HOH A 13 2013 2013 HOH HOH . H 5 HOH A 14 2014 2014 HOH HOH . H 5 HOH A 15 2015 2015 HOH HOH . H 5 HOH A 16 2016 2016 HOH HOH . H 5 HOH A 17 2017 2017 HOH HOH . H 5 HOH A 18 2018 2018 HOH HOH . H 5 HOH A 19 2019 2019 HOH HOH . H 5 HOH A 20 2020 2020 HOH HOH . H 5 HOH A 21 2021 2021 HOH HOH . H 5 HOH A 22 2022 2022 HOH HOH . H 5 HOH A 23 2023 2023 HOH HOH . H 5 HOH A 24 2024 2024 HOH HOH . H 5 HOH A 25 2025 2025 HOH HOH . H 5 HOH A 26 2026 2026 HOH HOH . H 5 HOH A 27 2027 2027 HOH HOH . H 5 HOH A 28 2028 2028 HOH HOH . H 5 HOH A 29 2029 2029 HOH HOH . H 5 HOH A 30 2030 2030 HOH HOH . H 5 HOH A 31 2031 2031 HOH HOH . H 5 HOH A 32 2032 2032 HOH HOH . H 5 HOH A 33 2033 2033 HOH HOH . H 5 HOH A 34 2034 2034 HOH HOH . H 5 HOH A 35 2035 2035 HOH HOH . H 5 HOH A 36 2036 2036 HOH HOH . H 5 HOH A 37 2037 2037 HOH HOH . H 5 HOH A 38 2038 2038 HOH HOH . H 5 HOH A 39 2039 2039 HOH HOH . H 5 HOH A 40 2040 2040 HOH HOH . H 5 HOH A 41 2041 2041 HOH HOH . H 5 HOH A 42 2042 2042 HOH HOH . H 5 HOH A 43 2043 2043 HOH HOH . H 5 HOH A 44 2044 2044 HOH HOH . H 5 HOH A 45 2045 2045 HOH HOH . H 5 HOH A 46 2046 2046 HOH HOH . H 5 HOH A 47 2047 2047 HOH HOH . H 5 HOH A 48 2048 2048 HOH HOH . H 5 HOH A 49 2049 2049 HOH HOH . H 5 HOH A 50 2050 2050 HOH HOH . H 5 HOH A 51 2051 2051 HOH HOH . H 5 HOH A 52 2052 2052 HOH HOH . H 5 HOH A 53 2053 2053 HOH HOH . H 5 HOH A 54 2054 2054 HOH HOH . H 5 HOH A 55 2055 2055 HOH HOH . H 5 HOH A 56 2056 2056 HOH HOH . H 5 HOH A 57 2057 2057 HOH HOH . H 5 HOH A 58 2058 2058 HOH HOH . H 5 HOH A 59 2059 2059 HOH HOH . H 5 HOH A 60 2060 2060 HOH HOH . H 5 HOH A 61 2061 2061 HOH HOH . H 5 HOH A 62 2062 2062 HOH HOH . H 5 HOH A 63 2063 2063 HOH HOH . H 5 HOH A 64 2064 2064 HOH HOH . H 5 HOH A 65 2065 2065 HOH HOH . H 5 HOH A 66 2066 2066 HOH HOH . H 5 HOH A 67 2067 2067 HOH HOH . I 5 HOH B 1 2001 2001 HOH HOH . I 5 HOH B 2 2002 2002 HOH HOH . I 5 HOH B 3 2003 2003 HOH HOH . I 5 HOH B 4 2004 2004 HOH HOH . I 5 HOH B 5 2005 2005 HOH HOH . I 5 HOH B 6 2006 2006 HOH HOH . I 5 HOH B 7 2007 2007 HOH HOH . I 5 HOH B 8 2008 2008 HOH HOH . I 5 HOH B 9 2009 2009 HOH HOH . I 5 HOH B 10 2010 2010 HOH HOH . I 5 HOH B 11 2011 2011 HOH HOH . I 5 HOH B 12 2012 2012 HOH HOH . I 5 HOH B 13 2013 2013 HOH HOH . I 5 HOH B 14 2014 2014 HOH HOH . I 5 HOH B 15 2015 2015 HOH HOH . I 5 HOH B 16 2016 2016 HOH HOH . I 5 HOH B 17 2017 2017 HOH HOH . I 5 HOH B 18 2018 2018 HOH HOH . I 5 HOH B 19 2019 2019 HOH HOH . I 5 HOH B 20 2020 2020 HOH HOH . I 5 HOH B 21 2021 2021 HOH HOH . I 5 HOH B 22 2022 2022 HOH HOH . I 5 HOH B 23 2023 2023 HOH HOH . I 5 HOH B 24 2024 2024 HOH HOH . I 5 HOH B 25 2025 2025 HOH HOH . I 5 HOH B 26 2026 2026 HOH HOH . I 5 HOH B 27 2027 2027 HOH HOH . I 5 HOH B 28 2028 2028 HOH HOH . I 5 HOH B 29 2029 2029 HOH HOH . I 5 HOH B 30 2030 2030 HOH HOH . I 5 HOH B 31 2031 2031 HOH HOH . I 5 HOH B 32 2032 2032 HOH HOH . I 5 HOH B 33 2033 2033 HOH HOH . I 5 HOH B 34 2034 2034 HOH HOH . I 5 HOH B 35 2035 2035 HOH HOH . I 5 HOH B 36 2036 2036 HOH HOH . I 5 HOH B 37 2037 2037 HOH HOH . I 5 HOH B 38 2038 2038 HOH HOH . I 5 HOH B 39 2039 2039 HOH HOH . I 5 HOH B 40 2040 2040 HOH HOH . I 5 HOH B 41 2041 2041 HOH HOH . I 5 HOH B 42 2042 2042 HOH HOH . I 5 HOH B 43 2043 2043 HOH HOH . I 5 HOH B 44 2044 2044 HOH HOH . I 5 HOH B 45 2045 2045 HOH HOH . I 5 HOH B 46 2046 2046 HOH HOH . I 5 HOH B 47 2047 2047 HOH HOH . I 5 HOH B 48 2048 2048 HOH HOH . I 5 HOH B 49 2049 2049 HOH HOH . I 5 HOH B 50 2050 2050 HOH HOH . I 5 HOH B 51 2051 2051 HOH HOH . I 5 HOH B 52 2052 2052 HOH HOH . I 5 HOH B 53 2053 2053 HOH HOH . I 5 HOH B 54 2054 2054 HOH HOH . I 5 HOH B 55 2055 2055 HOH HOH . I 5 HOH B 56 2056 2056 HOH HOH . I 5 HOH B 57 2057 2057 HOH HOH . I 5 HOH B 58 2058 2058 HOH HOH . I 5 HOH B 59 2059 2059 HOH HOH . I 5 HOH B 60 2060 2060 HOH HOH . I 5 HOH B 61 2061 2061 HOH HOH . I 5 HOH B 62 2062 2062 HOH HOH . I 5 HOH B 63 2063 2063 HOH HOH . I 5 HOH B 64 2064 2064 HOH HOH . I 5 HOH B 65 2065 2065 HOH HOH . I 5 HOH B 66 2066 2066 HOH HOH . I 5 HOH B 67 2067 2067 HOH HOH . I 5 HOH B 68 2068 2068 HOH HOH . I 5 HOH B 69 2069 2069 HOH HOH . I 5 HOH B 70 2070 2070 HOH HOH . I 5 HOH B 71 2071 2071 HOH HOH . I 5 HOH B 72 2072 2072 HOH HOH . I 5 HOH B 73 2073 2073 HOH HOH . I 5 HOH B 74 2074 2074 HOH HOH . I 5 HOH B 75 2075 2075 HOH HOH . I 5 HOH B 76 2076 2076 HOH HOH . I 5 HOH B 77 2077 2077 HOH HOH . I 5 HOH B 78 2078 2078 HOH HOH . I 5 HOH B 79 2079 2079 HOH HOH . I 5 HOH B 80 2080 2080 HOH HOH . I 5 HOH B 81 2081 2081 HOH HOH . I 5 HOH B 82 2082 2082 HOH HOH . I 5 HOH B 83 2083 2083 HOH HOH . I 5 HOH B 84 2084 2084 HOH HOH . I 5 HOH B 85 2085 2085 HOH HOH . J 5 HOH C 1 2001 2001 HOH HOH . K 5 HOH D 1 2001 2001 HOH HOH . K 5 HOH D 2 2002 2002 HOH HOH . K 5 HOH D 3 2003 2003 HOH HOH . K 5 HOH D 4 2004 2004 HOH HOH . K 5 HOH D 5 2005 2005 HOH HOH . K 5 HOH D 6 2006 2006 HOH HOH . K 5 HOH D 7 2007 2007 HOH HOH . K 5 HOH D 8 2008 2008 HOH HOH . K 5 HOH D 9 2009 2009 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 P PA TYD . . . E 3 42.165 79.556 27.841 1 41.04 ? PA TYD 406 A 1 HETATM 2 O O1A TYD . . . E 3 41.312 80.381 28.726 1 41.7 ? O1A TYD 406 A 1 HETATM 3 O O2A TYD . . . E 3 42.976 78.476 28.448 1 40.64 ? O2A TYD 406 A 1 HETATM 4 O O3A TYD . . . E 3 43.201 80.647 27.2 1 40.09 ? O3A TYD 406 A 1 HETATM 5 P PB TYD . . . E 3 44.515 80.627 26.231 1 39.44 ? PB TYD 406 A 1 HETATM 6 O O1B TYD . . . E 3 44.122 81.214 24.888 1 35.12 ? O1B TYD 406 A 1 HETATM 7 O O2B TYD . . . E 3 44.936 79.172 26.142 1 38.34 ? O2B TYD 406 A 1 HETATM 8 O O3B TYD . . . E 3 45.533 81.503 26.946 1 40.31 ? O3B TYD 406 A 1 HETATM 9 O O5' TYD . . . E 3 41.218 78.887 26.731 1 39.89 ? O5' TYD 406 A 1 HETATM 10 C C5' TYD . . . E 3 40.198 79.647 26.082 1 39.55 ? C5' TYD 406 A 1 HETATM 11 C C4' TYD . . . E 3 39.047 78.764 25.617 1 39.33 ? C4' TYD 406 A 1 HETATM 12 O O4' TYD . . . E 3 39.356 77.973 24.452 1 38.69 ? O4' TYD 406 A 1 HETATM 13 C C3' TYD . . . E 3 38.549 77.704 26.584 1 39.33 ? C3' TYD 406 A 1 HETATM 14 O O3' TYD . . . E 3 37.645 78.269 27.525 1 41.57 ? O3' TYD 406 A 1 HETATM 15 C C2' TYD . . . E 3 37.801 76.709 25.689 1 38.52 ? C2' TYD 406 A 1 HETATM 16 C C1' TYD . . . E 3 38.302 77.05 24.282 1 38.51 ? C1' TYD 406 A 1 HETATM 17 N N1 TYD . . . E 3 38.761 75.899 23.483 1 39.03 ? N1 TYD 406 A 1 HETATM 18 C C2 TYD . . . E 3 37.801 75.204 22.781 1 40.28 ? C2 TYD 406 A 1 HETATM 19 O O2 TYD . . . E 3 36.609 75.384 22.93 1 42.14 ? O2 TYD 406 A 1 HETATM 20 N N3 TYD . . . E 3 38.291 74.284 21.894 1 40.94 ? N3 TYD 406 A 1 HETATM 21 C C4 TYD . . . E 3 39.614 73.997 21.635 1 40.98 ? C4 TYD 406 A 1 HETATM 22 O O4 TYD . . . E 3 39.9 73.149 20.792 1 41.3 ? O4 TYD 406 A 1 HETATM 23 C C5 TYD . . . E 3 40.572 74.758 22.408 1 39.87 ? C5 TYD 406 A 1 HETATM 24 C C5M TYD . . . E 3 42.032 74.512 22.203 1 38.71 ? C5M TYD 406 A 1 HETATM 25 C C6 TYD . . . E 3 40.101 75.657 23.283 1 39.77 ? C6 TYD 406 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #