data_1CXZ # _model_server_result.job_id i5Pg7lNpkfEr_foLz82yow _model_server_result.datetime_utc '2024-11-02 21:33:14' _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 1cxz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1CXZ # _exptl.entry_id 1CXZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 1CXZ _cell.length_a 66.9 _cell.length_b 66.9 _cell.length_c 149.5 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1CXZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 4 _struct_asym.id D _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 OG1 THR 20 A THR 19 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc2 A OG1 THR 38 A THR 37 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc3 D O2B GSP . A GSP 500 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc4 D O2G GSP . A GSP 500 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc5 C MG MG . A MG 501 1_555 E O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc6 C MG MG . A MG 501 1_555 E O HOH . A HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GSP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 O3B GSP sing 129 n n PG S1G GSP doub 130 n n PG O2G GSP sing 131 n n PG O3G GSP sing 132 n n O3B PB GSP sing 133 n n O2G HOG2 GSP sing 134 n n O3G HOG3 GSP sing 135 n n PB O1B GSP doub 136 n n PB O2B GSP sing 137 n n PB O3A GSP sing 138 n n O2B HOB2 GSP sing 139 n n PA O1A GSP doub 140 n n PA O2A GSP sing 141 n n PA O3A GSP sing 142 n n PA O5' GSP sing 143 n n O2A HOA2 GSP sing 144 n n O5' C5' GSP sing 145 n n C5' C4' GSP sing 146 n n C5' "H5'1" GSP sing 147 n n C5' "H5'2" GSP sing 148 n n C4' O4' GSP sing 149 n n C4' C3' GSP sing 150 n n C4' H4' GSP sing 151 n n O4' C1' GSP sing 152 n n C3' O3' GSP sing 153 n n C3' C2' GSP sing 154 n n C3' H3' GSP sing 155 n n O3' HO3' GSP sing 156 n n C2' O2' GSP sing 157 n n C2' C1' GSP sing 158 n n C2' H2' GSP sing 159 n n O2' HO2' GSP sing 160 n n C1' N9 GSP sing 161 n n C1' H1' GSP sing 162 n n N9 C8 GSP sing 163 n y N9 C4 GSP sing 164 n y C8 N7 GSP doub 165 n y C8 H8 GSP sing 166 n n N7 C5 GSP sing 167 n y C5 C6 GSP sing 168 n n C5 C4 GSP doub 169 n y C6 O6 GSP doub 170 n n C6 N1 GSP sing 171 n n N1 C2 GSP sing 172 n n N1 HN1 GSP sing 173 n n C2 N2 GSP sing 174 n n C2 N3 GSP doub 175 n n N2 HN21 GSP sing 176 n n N2 HN22 GSP sing 177 n n N3 C4 GSP sing 178 n n # _atom_sites.entry_id 1CXZ _atom_sites.fract_transf_matrix[1][1] 0.014948 _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] 0.014948 _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] 0.006689 _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 3 MG A 1 501 501 MG MG . D 4 GSP A 1 500 500 GSP GSP . E 5 HOH A 1 2001 2001 HOH TIP . E 5 HOH A 2 2002 2002 HOH TIP . E 5 HOH A 3 2003 2003 HOH TIP . E 5 HOH A 4 2004 2004 HOH TIP . E 5 HOH A 5 2005 2005 HOH TIP . E 5 HOH A 6 2006 2006 HOH TIP . E 5 HOH A 7 2007 2007 HOH TIP . E 5 HOH A 8 2008 2008 HOH TIP . E 5 HOH A 9 2009 2009 HOH TIP . E 5 HOH A 10 2012 2012 HOH TIP . E 5 HOH A 11 2013 2013 HOH TIP . E 5 HOH A 12 2014 2014 HOH TIP . E 5 HOH A 13 2015 2015 HOH TIP . E 5 HOH A 14 2016 2016 HOH TIP . E 5 HOH A 15 2017 2017 HOH TIP . E 5 HOH A 16 2019 2019 HOH TIP . E 5 HOH A 17 2020 2020 HOH TIP . E 5 HOH A 18 2021 2021 HOH TIP . E 5 HOH A 19 2022 2022 HOH TIP . E 5 HOH A 20 2023 2023 HOH TIP . E 5 HOH A 21 2024 2024 HOH TIP . E 5 HOH A 22 2025 2025 HOH TIP . E 5 HOH A 23 2026 2026 HOH TIP . E 5 HOH A 24 2027 2027 HOH TIP . E 5 HOH A 25 2029 2029 HOH TIP . E 5 HOH A 26 2030 2030 HOH TIP . E 5 HOH A 27 2031 2031 HOH TIP . E 5 HOH A 28 2032 2032 HOH TIP . E 5 HOH A 29 2033 2033 HOH TIP . E 5 HOH A 30 2034 2034 HOH TIP . E 5 HOH A 31 2035 2035 HOH TIP . E 5 HOH A 32 2037 2037 HOH TIP . E 5 HOH A 33 2038 2038 HOH TIP . E 5 HOH A 34 2039 2039 HOH TIP . E 5 HOH A 35 2040 2040 HOH TIP . E 5 HOH A 36 2041 2041 HOH TIP . E 5 HOH A 37 2042 2042 HOH TIP . E 5 HOH A 38 2043 2043 HOH TIP . E 5 HOH A 39 2044 2044 HOH TIP . E 5 HOH A 40 2045 2045 HOH TIP . E 5 HOH A 41 2046 2046 HOH TIP . E 5 HOH A 42 2048 2048 HOH TIP . E 5 HOH A 43 2049 2049 HOH TIP . E 5 HOH A 44 2050 2050 HOH TIP . E 5 HOH A 45 2051 2051 HOH TIP . E 5 HOH A 46 2054 2054 HOH TIP . E 5 HOH A 47 2056 2056 HOH TIP . E 5 HOH A 48 2057 2057 HOH TIP . E 5 HOH A 49 2060 2060 HOH TIP . E 5 HOH A 50 2061 2061 HOH TIP . E 5 HOH A 51 2062 2062 HOH TIP . E 5 HOH A 52 2063 2063 HOH TIP . E 5 HOH A 53 2064 2064 HOH TIP . E 5 HOH A 54 2066 2066 HOH TIP . E 5 HOH A 55 2067 2067 HOH TIP . E 5 HOH A 56 2068 2068 HOH TIP . E 5 HOH A 57 2069 2069 HOH TIP . E 5 HOH A 58 2071 2071 HOH TIP . E 5 HOH A 59 2073 2073 HOH TIP . E 5 HOH A 60 2075 2075 HOH TIP . E 5 HOH A 61 2076 2076 HOH TIP . E 5 HOH A 62 2077 2077 HOH TIP . E 5 HOH A 63 2078 2078 HOH TIP . E 5 HOH A 64 2079 2079 HOH TIP . E 5 HOH A 65 2080 2080 HOH TIP . E 5 HOH A 66 2082 2082 HOH TIP . E 5 HOH A 67 2083 2083 HOH TIP . E 5 HOH A 68 2084 2084 HOH TIP . E 5 HOH A 69 2085 2085 HOH TIP . E 5 HOH A 70 2086 2086 HOH TIP . E 5 HOH A 71 2087 2087 HOH TIP . E 5 HOH A 72 2088 2088 HOH TIP . E 5 HOH A 73 2090 2090 HOH TIP . E 5 HOH A 74 2091 2091 HOH TIP . E 5 HOH A 75 2092 2092 HOH TIP . E 5 HOH A 76 2093 2093 HOH TIP . E 5 HOH A 77 2094 2094 HOH TIP . E 5 HOH A 78 2095 2095 HOH TIP . E 5 HOH A 79 2096 2096 HOH TIP . E 5 HOH A 80 2097 2097 HOH TIP . E 5 HOH A 81 2098 2098 HOH TIP . E 5 HOH A 82 2099 2099 HOH TIP . E 5 HOH A 83 2101 2101 HOH TIP . E 5 HOH A 84 2102 2102 HOH TIP . E 5 HOH A 85 2103 2103 HOH TIP . E 5 HOH A 86 2104 2104 HOH TIP . E 5 HOH A 87 2105 2105 HOH TIP . E 5 HOH A 88 2106 2106 HOH TIP . E 5 HOH A 89 2108 2108 HOH TIP . E 5 HOH A 90 2109 2109 HOH TIP . E 5 HOH A 91 2110 2110 HOH TIP . E 5 HOH A 92 2112 2112 HOH TIP . E 5 HOH A 93 2113 2113 HOH TIP . E 5 HOH A 94 2115 2115 HOH TIP . E 5 HOH A 95 2116 2116 HOH TIP . E 5 HOH A 96 2117 2117 HOH TIP . E 5 HOH A 97 2120 2120 HOH TIP . E 5 HOH A 98 2121 2121 HOH TIP . F 5 HOH B 1 2010 2010 HOH TIP . F 5 HOH B 2 2011 2011 HOH TIP . F 5 HOH B 3 2018 2018 HOH TIP . F 5 HOH B 4 2036 2036 HOH TIP . F 5 HOH B 5 2047 2047 HOH TIP . F 5 HOH B 6 2052 2052 HOH TIP . F 5 HOH B 7 2055 2055 HOH TIP . F 5 HOH B 8 2058 2058 HOH TIP . F 5 HOH B 9 2059 2059 HOH TIP . F 5 HOH B 10 2065 2065 HOH TIP . F 5 HOH B 11 2072 2072 HOH TIP . F 5 HOH B 12 2074 2074 HOH TIP . F 5 HOH B 13 2081 2081 HOH TIP . F 5 HOH B 14 2089 2089 HOH TIP . F 5 HOH B 15 2100 2100 HOH TIP . F 5 HOH B 16 2111 2111 HOH TIP . F 5 HOH B 17 2119 2119 HOH TIP . # 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 GSP . . . D 4 11.955 28.208 48.887 1 24.21 ? PG GSP 500 A 1 HETATM 2 O O3B GSP . . . D 4 10.468 28.817 49.337 1 23.91 ? O3B GSP 500 A 1 HETATM 3 S S1G GSP . . . D 4 13.151 29.732 48.789 1 29.24 ? S1G GSP 500 A 1 HETATM 4 O O2G GSP . . . D 4 12.286 27.265 49.975 1 23.18 ? O2G GSP 500 A 1 HETATM 5 O O3G GSP . . . D 4 11.662 27.577 47.557 1 26.26 ? O3G GSP 500 A 1 HETATM 6 P PB GSP . . . D 4 9.031 28.133 49.481 1 21.41 ? PB GSP 500 A 1 HETATM 7 O O1B GSP . . . D 4 8.436 28.118 48.152 1 23.85 ? O1B GSP 500 A 1 HETATM 8 O O2B GSP . . . D 4 9.006 26.83 50.227 1 24.17 ? O2B GSP 500 A 1 HETATM 9 P PA GSP . . . D 4 7.589 29.134 51.835 1 23.05 ? PA GSP 500 A 1 HETATM 10 O O1A GSP . . . D 4 6.562 28.081 51.802 1 23.77 ? O1A GSP 500 A 1 HETATM 11 O O2A GSP . . . D 4 8.692 29 52.834 1 27.11 ? O2A GSP 500 A 1 HETATM 12 O O3A GSP . . . D 4 8.195 29.193 50.333 1 25.42 ? O3A GSP 500 A 1 HETATM 13 O O5' GSP . . . D 4 6.907 30.59 51.916 1 26.02 ? O5' GSP 500 A 1 HETATM 14 C C5' GSP . . . D 4 7.537 31.795 51.505 1 25.48 ? C5' GSP 500 A 1 HETATM 15 C C4' GSP . . . D 4 6.954 32.982 52.184 1 26.34 ? C4' GSP 500 A 1 HETATM 16 O O4' GSP . . . D 4 5.547 33.129 51.834 1 26.42 ? O4' GSP 500 A 1 HETATM 17 C C3' GSP . . . D 4 6.988 32.797 53.694 1 26.82 ? C3' GSP 500 A 1 HETATM 18 O O3' GSP . . . D 4 7.289 34.024 54.377 1 30.11 ? O3' GSP 500 A 1 HETATM 19 C C2' GSP . . . D 4 5.562 32.316 54.053 1 25.97 ? C2' GSP 500 A 1 HETATM 20 O O2' GSP . . . D 4 5.137 32.656 55.355 1 25.81 ? O2' GSP 500 A 1 HETATM 21 C C1' GSP . . . D 4 4.688 32.996 53.001 1 25.63 ? C1' GSP 500 A 1 HETATM 22 N N9 GSP . . . D 4 3.538 32.139 52.652 1 26.13 ? N9 GSP 500 A 1 HETATM 23 C C8 GSP . . . D 4 3.497 30.78 52.383 1 24.59 ? C8 GSP 500 A 1 HETATM 24 N N7 GSP . . . D 4 2.332 30.316 52.112 1 24.6 ? N7 GSP 500 A 1 HETATM 25 C C5 GSP . . . D 4 1.517 31.447 52.206 1 25.38 ? C5 GSP 500 A 1 HETATM 26 C C6 GSP . . . D 4 0.08 31.592 52.016 1 25.94 ? C6 GSP 500 A 1 HETATM 27 O O6 GSP . . . D 4 -0.767 30.744 51.724 1 25.72 ? O6 GSP 500 A 1 HETATM 28 N N1 GSP . . . D 4 -0.325 32.914 52.204 1 25.68 ? N1 GSP 500 A 1 HETATM 29 C C2 GSP . . . D 4 0.512 33.952 52.531 1 25.15 ? C2 GSP 500 A 1 HETATM 30 N N2 GSP . . . D 4 0.007 35.158 52.678 1 25.72 ? N2 GSP 500 A 1 HETATM 31 N N3 GSP . . . D 4 1.823 33.816 52.711 1 25.41 ? N3 GSP 500 A 1 HETATM 32 C C4 GSP . . . D 4 2.257 32.544 52.529 1 25.9 ? C4 GSP 500 A 1 # _model_server_stats.io_time_ms 37 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #