data_1W58 # _model_server_result.job_id k3_adVUTkd4cK2kikF08Ig _model_server_result.datetime_utc '2024-11-04 23:47:31' _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 1w58 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1362}' # _entry.id 1W58 # _exptl.entry_id 1W58 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 521.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _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 1W58 _cell.length_a 161.16 _cell.length_b 161.16 _cell.length_c 161.16 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1W58 _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PQS _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 _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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 NE2 GLN 75 1 GLN 75 1_555 C MG MG . 1 MG 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc2 B O3G G2P . 1 G2P 1362 1_555 C MG MG . 1 MG 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc3 B O2G G2P . 1 G2P 1362 1_555 C MG MG . 1 MG 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc4 B O2B G2P . 1 G2P 1362 1_555 C MG MG . 1 MG 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc5 C MG MG . 1 MG 1363 1_555 D O HOH . 1 HOH 2023 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc6 C MG MG . 1 MG 1363 1_555 D O HOH . 1 HOH 2136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? # _chem_comp.formula 'C11 H18 N5 O13 P3' _chem_comp.formula_weight 521.208 _chem_comp.id G2P _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _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 PG O1G G2P sing 83 n n PG O2G G2P doub 84 n n PG O3G G2P sing 85 n n PG O3B G2P sing 86 n n O3B PB G2P sing 87 n n PB O1B G2P sing 88 n n PB O2B G2P doub 89 n n PB C3A G2P sing 90 n n C3A PA G2P sing 91 n n C3A H3A1 G2P sing 92 n n C3A H3A2 G2P sing 93 n n PA O1A G2P sing 94 n n PA O2A G2P doub 95 n n PA O5' G2P sing 96 n n O5' C5' G2P sing 97 n n C5' C4' G2P sing 98 n n C5' "H5'1" G2P sing 99 n n C5' "H5'2" G2P sing 100 n n C4' O4' G2P sing 101 n n C4' C3' G2P sing 102 n n C4' H4' G2P sing 103 n n O4' C1' G2P sing 104 n n C3' O3' G2P sing 105 n n C3' C2' G2P sing 106 n n C3' H3' G2P sing 107 n n O3' HA G2P sing 108 n n C2' O2' G2P sing 109 n n C2' C1' G2P sing 110 n n C2' H2' G2P sing 111 n n O2' HB G2P sing 112 n n C1' N9 G2P sing 113 n n C1' H1' G2P sing 114 n n N9 C8 G2P sing 115 n y N9 C4 G2P sing 116 n y C8 N7 G2P doub 117 n y C8 H8 G2P sing 118 n n N7 C5 G2P sing 119 n y C5 C6 G2P sing 120 n y C5 C4 G2P doub 121 n y C6 O6 G2P doub 122 n n C6 N1 G2P sing 123 n y N1 C2 G2P sing 124 n y N1 H1 G2P sing 125 n n C2 N2 G2P sing 126 n n C2 N3 G2P doub 127 n y N2 H2N1 G2P sing 128 n n N2 H2N2 G2P sing 129 n n N3 C4 G2P sing 130 n y HO1 O1G G2P sing 131 n n HO2 O3G G2P sing 132 n n HO3 O1A G2P sing 133 n n HO4 O1B G2P sing 134 n n # _atom_sites.entry_id 1W58 _atom_sites.fract_transf_matrix[1][1] 0.006205 _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] 0.006205 _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] 0.006205 _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 G2P 1 1 1362 1362 G2P G2P . C 3 MG 1 1 1363 1363 MG MG . D 4 HOH 1 1 2001 2001 HOH HOH . D 4 HOH 1 2 2002 2002 HOH HOH . D 4 HOH 1 3 2003 2003 HOH HOH . D 4 HOH 1 4 2004 2004 HOH HOH . D 4 HOH 1 5 2005 2005 HOH HOH . D 4 HOH 1 6 2006 2006 HOH HOH . D 4 HOH 1 7 2007 2007 HOH HOH . D 4 HOH 1 8 2008 2008 HOH HOH . D 4 HOH 1 9 2009 2009 HOH HOH . D 4 HOH 1 10 2010 2010 HOH HOH . D 4 HOH 1 11 2011 2011 HOH HOH . D 4 HOH 1 12 2012 2012 HOH HOH . D 4 HOH 1 13 2013 2013 HOH HOH . D 4 HOH 1 14 2014 2014 HOH HOH . D 4 HOH 1 15 2015 2015 HOH HOH . D 4 HOH 1 16 2016 2016 HOH HOH . D 4 HOH 1 17 2017 2017 HOH HOH . D 4 HOH 1 18 2018 2018 HOH HOH . D 4 HOH 1 19 2019 2019 HOH HOH . D 4 HOH 1 20 2020 2020 HOH HOH . D 4 HOH 1 21 2021 2021 HOH HOH . D 4 HOH 1 22 2022 2022 HOH HOH . D 4 HOH 1 23 2023 2023 HOH HOH . D 4 HOH 1 24 2024 2024 HOH HOH . D 4 HOH 1 25 2025 2025 HOH HOH . D 4 HOH 1 26 2026 2026 HOH HOH . D 4 HOH 1 27 2027 2027 HOH HOH . D 4 HOH 1 28 2028 2028 HOH HOH . D 4 HOH 1 29 2029 2029 HOH HOH . D 4 HOH 1 30 2030 2030 HOH HOH . D 4 HOH 1 31 2031 2031 HOH HOH . D 4 HOH 1 32 2032 2032 HOH HOH . D 4 HOH 1 33 2033 2033 HOH HOH . D 4 HOH 1 34 2034 2034 HOH HOH . D 4 HOH 1 35 2035 2035 HOH HOH . D 4 HOH 1 36 2036 2036 HOH HOH . D 4 HOH 1 37 2037 2037 HOH HOH . D 4 HOH 1 38 2038 2038 HOH HOH . D 4 HOH 1 39 2039 2039 HOH HOH . D 4 HOH 1 40 2040 2040 HOH HOH . D 4 HOH 1 41 2041 2041 HOH HOH . D 4 HOH 1 42 2042 2042 HOH HOH . D 4 HOH 1 43 2043 2043 HOH HOH . D 4 HOH 1 44 2044 2044 HOH HOH . D 4 HOH 1 45 2045 2045 HOH HOH . D 4 HOH 1 46 2046 2046 HOH HOH . D 4 HOH 1 47 2047 2047 HOH HOH . D 4 HOH 1 48 2048 2048 HOH HOH . D 4 HOH 1 49 2049 2049 HOH HOH . D 4 HOH 1 50 2050 2050 HOH HOH . D 4 HOH 1 51 2051 2051 HOH HOH . D 4 HOH 1 52 2052 2052 HOH HOH . D 4 HOH 1 53 2053 2053 HOH HOH . D 4 HOH 1 54 2054 2054 HOH HOH . D 4 HOH 1 55 2055 2055 HOH HOH . D 4 HOH 1 56 2056 2056 HOH HOH . D 4 HOH 1 57 2057 2057 HOH HOH . D 4 HOH 1 58 2058 2058 HOH HOH . D 4 HOH 1 59 2059 2059 HOH HOH . D 4 HOH 1 60 2060 2060 HOH HOH . D 4 HOH 1 61 2061 2061 HOH HOH . D 4 HOH 1 62 2062 2062 HOH HOH . D 4 HOH 1 63 2063 2063 HOH HOH . D 4 HOH 1 64 2064 2064 HOH HOH . D 4 HOH 1 65 2065 2065 HOH HOH . D 4 HOH 1 66 2066 2066 HOH HOH . D 4 HOH 1 67 2067 2067 HOH HOH . D 4 HOH 1 68 2068 2068 HOH HOH . D 4 HOH 1 69 2069 2069 HOH HOH . D 4 HOH 1 70 2070 2070 HOH HOH . D 4 HOH 1 71 2071 2071 HOH HOH . D 4 HOH 1 72 2072 2072 HOH HOH . D 4 HOH 1 73 2073 2073 HOH HOH . D 4 HOH 1 74 2074 2074 HOH HOH . D 4 HOH 1 75 2075 2075 HOH HOH . D 4 HOH 1 76 2076 2076 HOH HOH . D 4 HOH 1 77 2077 2077 HOH HOH . D 4 HOH 1 78 2078 2078 HOH HOH . D 4 HOH 1 79 2079 2079 HOH HOH . D 4 HOH 1 80 2080 2080 HOH HOH . D 4 HOH 1 81 2081 2081 HOH HOH . D 4 HOH 1 82 2082 2082 HOH HOH . D 4 HOH 1 83 2083 2083 HOH HOH . D 4 HOH 1 84 2084 2084 HOH HOH . D 4 HOH 1 85 2085 2085 HOH HOH . D 4 HOH 1 86 2086 2086 HOH HOH . D 4 HOH 1 87 2087 2087 HOH HOH . D 4 HOH 1 88 2088 2088 HOH HOH . D 4 HOH 1 89 2089 2089 HOH HOH . D 4 HOH 1 90 2090 2090 HOH HOH . D 4 HOH 1 91 2091 2091 HOH HOH . D 4 HOH 1 92 2092 2092 HOH HOH . D 4 HOH 1 93 2093 2093 HOH HOH . D 4 HOH 1 94 2094 2094 HOH HOH . D 4 HOH 1 95 2095 2095 HOH HOH . D 4 HOH 1 96 2096 2096 HOH HOH . D 4 HOH 1 97 2097 2097 HOH HOH . D 4 HOH 1 98 2098 2098 HOH HOH . D 4 HOH 1 99 2099 2099 HOH HOH . D 4 HOH 1 100 2100 2100 HOH HOH . D 4 HOH 1 101 2101 2101 HOH HOH . D 4 HOH 1 102 2102 2102 HOH HOH . D 4 HOH 1 103 2103 2103 HOH HOH . D 4 HOH 1 104 2104 2104 HOH HOH . D 4 HOH 1 105 2105 2105 HOH HOH . D 4 HOH 1 106 2106 2106 HOH HOH . D 4 HOH 1 107 2107 2107 HOH HOH . D 4 HOH 1 108 2108 2108 HOH HOH . D 4 HOH 1 109 2109 2109 HOH HOH . D 4 HOH 1 110 2110 2110 HOH HOH . D 4 HOH 1 111 2111 2111 HOH HOH . D 4 HOH 1 112 2112 2112 HOH HOH . D 4 HOH 1 113 2113 2113 HOH HOH . D 4 HOH 1 114 2114 2114 HOH HOH . D 4 HOH 1 115 2115 2115 HOH HOH . D 4 HOH 1 116 2116 2116 HOH HOH . D 4 HOH 1 117 2117 2117 HOH HOH . D 4 HOH 1 118 2118 2118 HOH HOH . D 4 HOH 1 119 2119 2119 HOH HOH . D 4 HOH 1 120 2120 2120 HOH HOH . D 4 HOH 1 121 2121 2121 HOH HOH . D 4 HOH 1 122 2122 2122 HOH HOH . D 4 HOH 1 123 2123 2123 HOH HOH . D 4 HOH 1 124 2124 2124 HOH HOH . D 4 HOH 1 125 2125 2125 HOH HOH . D 4 HOH 1 126 2126 2126 HOH HOH . D 4 HOH 1 127 2127 2127 HOH HOH . D 4 HOH 1 128 2128 2128 HOH HOH . D 4 HOH 1 129 2129 2129 HOH HOH . D 4 HOH 1 130 2130 2130 HOH HOH . D 4 HOH 1 131 2131 2131 HOH HOH . D 4 HOH 1 132 2132 2132 HOH HOH . D 4 HOH 1 133 2133 2133 HOH HOH . D 4 HOH 1 134 2134 2134 HOH HOH . D 4 HOH 1 135 2135 2135 HOH HOH . D 4 HOH 1 136 2136 2136 HOH HOH . D 4 HOH 1 137 2137 2137 HOH HOH . D 4 HOH 1 138 2138 2138 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 PG G2P . . . B 2 4.755 36.871 1.293 1 59.04 ? PG G2P 1362 1 1 HETATM 2 O O1G G2P . . . B 2 4.715 37.452 2.633 1 55.99 ? O1G G2P 1362 1 1 HETATM 3 O O2G G2P . . . B 2 3.922 37.646 0.382 1 64.23 ? O2G G2P 1362 1 1 HETATM 4 O O3G G2P . . . B 2 4.077 35.479 1.293 1 60.61 ? O3G G2P 1362 1 1 HETATM 5 O O3B G2P . . . B 2 6.326 36.708 0.845 1 53.6 ? O3B G2P 1362 1 1 HETATM 6 P PB G2P . . . B 2 6.923 36.15 -0.599 1 39.5 ? PB G2P 1362 1 1 HETATM 7 O O1B G2P . . . B 2 8.123 35.342 -0.364 1 46.99 ? O1B G2P 1362 1 1 HETATM 8 O O2B G2P . . . B 2 6.021 35.475 -1.495 1 33.85 ? O2B G2P 1362 1 1 HETATM 9 C C3A G2P . . . B 2 7.527 37.631 -1.37 1 38.27 ? C3A G2P 1362 1 1 HETATM 10 P PA G2P . . . B 2 7.431 37.652 -3.159 1 40.37 ? PA G2P 1362 1 1 HETATM 11 O O1A G2P . . . B 2 7.741 36.355 -3.793 1 41.26 ? O1A G2P 1362 1 1 HETATM 12 O O2A G2P . . . B 2 6.256 38.366 -3.671 1 41.01 ? O2A G2P 1362 1 1 HETATM 13 O O5' G2P . . . B 2 8.765 38.486 -3.322 1 40.09 ? O5' G2P 1362 1 1 HETATM 14 C C5' G2P . . . B 2 8.993 39.776 -2.831 1 44.54 ? C5' G2P 1362 1 1 HETATM 15 C C4' G2P . . . B 2 10.373 40.252 -3.352 1 42.26 ? C4' G2P 1362 1 1 HETATM 16 O O4' G2P . . . B 2 10.816 39.438 -4.501 1 35.51 ? O4' G2P 1362 1 1 HETATM 17 C C3' G2P . . . B 2 10.266 41.711 -3.808 1 35.97 ? C3' G2P 1362 1 1 HETATM 18 O O3' G2P . . . B 2 10.868 42.521 -2.79 1 44.83 ? O3' G2P 1362 1 1 HETATM 19 C C2' G2P . . . B 2 10.965 41.727 -5.174 1 35.01 ? C2' G2P 1362 1 1 HETATM 20 O O2' G2P . . . B 2 12.29 42.2 -5.087 1 35.7 ? O2' G2P 1362 1 1 HETATM 21 C C1' G2P . . . B 2 10.976 40.282 -5.676 1 36.09 ? C1' G2P 1362 1 1 HETATM 22 N N9 G2P . . . B 2 9.855 40.015 -6.637 1 38.94 ? N9 G2P 1362 1 1 HETATM 23 C C8 G2P . . . B 2 8.483 40.172 -6.463 1 40.25 ? C8 G2P 1362 1 1 HETATM 24 N N7 G2P . . . B 2 7.748 39.85 -7.475 1 41.04 ? N7 G2P 1362 1 1 HETATM 25 C C5 G2P . . . B 2 8.671 39.434 -8.445 1 41.6 ? C5 G2P 1362 1 1 HETATM 26 C C6 G2P . . . B 2 8.478 38.945 -9.808 1 45.9 ? C6 G2P 1362 1 1 HETATM 27 O O6 G2P . . . B 2 7.417 38.784 -10.437 1 45.46 ? O6 G2P 1362 1 1 HETATM 28 N N1 G2P . . . B 2 9.699 38.635 -10.437 1 43.81 ? N1 G2P 1362 1 1 HETATM 29 C C2 G2P . . . B 2 10.96 38.762 -9.86 1 42.2 ? C2 G2P 1362 1 1 HETATM 30 N N2 G2P . . . B 2 12.03 38.42 -10.602 1 40.21 ? N2 G2P 1362 1 1 HETATM 31 N N3 G2P . . . B 2 11.135 39.212 -8.595 1 40.11 ? N3 G2P 1362 1 1 HETATM 32 C C4 G2P . . . B 2 9.974 39.531 -7.941 1 39.8 ? C4 G2P 1362 1 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #