data_2J5X # _model_server_result.job_id GXrcghC1-6kVbOxUW-onQA _model_server_result.datetime_utc '2024-11-22 22:48:53' _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 2j5x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":190}' # _entry.id 2J5X # _exptl.entry_id 2J5X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 2J5X _cell.length_a 72.895 _cell.length_b 72.895 _cell.length_c 131.489 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2J5X _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS monomeric 1 author_and_software_defined_assembly 1 PQS monomeric 1 author_and_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,D,G 1 1 B,E,F,H 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 27 A THR 27 1_555 D MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc2 A OG1 THR 44 A THR 44 1_555 D MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc3 C O3G GSP . A GSP 190 1_555 D MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.779 ? metalc ? metalc4 C O2B GSP . A GSP 190 1_555 D MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc5 D MG MG . A MG 200 1_555 G O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc6 D MG MG . A MG 200 1_555 G O HOH . A HOH 2010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc7 B OG1 THR 27 B THR 27 1_555 F MG MG . B MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc8 B OG1 THR 44 B THR 44 1_555 F MG MG . B MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc9 E O2B GSP . B GSP 190 1_555 F MG MG . B MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc10 E O3G GSP . B GSP 190 1_555 F MG MG . B MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc11 F MG MG . B MG 200 1_555 H O HOH . B HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc12 F MG MG . B MG 200 1_555 H O HOH . B HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? # _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 2J5X _atom_sites.fract_transf_matrix[1][1] 0.013718 _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] 0.013718 _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] 0.007605 _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 2 GSP A 1 190 190 GSP GSP . D 3 MG A 1 200 200 MG MG . E 2 GSP B 1 190 190 GSP GSP . F 3 MG B 1 200 200 MG MG . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . G 4 HOH A 4 2004 2004 HOH HOH . G 4 HOH A 5 2005 2005 HOH HOH . G 4 HOH A 6 2006 2006 HOH HOH . G 4 HOH A 7 2007 2007 HOH HOH . G 4 HOH A 8 2008 2008 HOH HOH . G 4 HOH A 9 2009 2009 HOH HOH . G 4 HOH A 10 2010 2010 HOH HOH . G 4 HOH A 11 2011 2011 HOH HOH . G 4 HOH A 12 2012 2012 HOH HOH . G 4 HOH A 13 2013 2013 HOH HOH . G 4 HOH A 14 2014 2014 HOH HOH . G 4 HOH A 15 2015 2015 HOH HOH . G 4 HOH A 16 2016 2016 HOH HOH . G 4 HOH A 17 2017 2017 HOH HOH . G 4 HOH A 18 2018 2018 HOH HOH . G 4 HOH A 19 2019 2019 HOH HOH . G 4 HOH A 20 2020 2020 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 HOH HOH . H 4 HOH B 6 2006 2006 HOH HOH . H 4 HOH B 7 2007 2007 HOH HOH . H 4 HOH B 8 2008 2008 HOH HOH . H 4 HOH B 9 2009 2009 HOH HOH . H 4 HOH B 10 2010 2010 HOH HOH . H 4 HOH B 11 2011 2011 HOH HOH . H 4 HOH B 12 2012 2012 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 GSP . . . E 2 74.726 37.497 19.59 1 32.2 ? PG GSP 190 B 1 HETATM 2 O O3B GSP . . . E 2 75.351 37.293 18.107 1 29.11 ? O3B GSP 190 B 1 HETATM 3 S S1G GSP . . . E 2 73.168 38.308 19.469 1 27.65 ? S1G GSP 190 B 1 HETATM 4 O O2G GSP . . . E 2 75.783 38.271 20.427 1 27.84 ? O2G GSP 190 B 1 HETATM 5 O O3G GSP . . . E 2 74.436 36.144 20.235 1 28.64 ? O3G GSP 190 B 1 HETATM 6 P PB GSP . . . E 2 76.719 36.481 17.859 1 28.65 ? PB GSP 190 B 1 HETATM 7 O O1B GSP . . . E 2 77.86 37.434 17.837 1 26.14 ? O1B GSP 190 B 1 HETATM 8 O O2B GSP . . . E 2 76.91 35.294 18.733 1 26.26 ? O2B GSP 190 B 1 HETATM 9 P PA GSP . . . E 2 76.023 34.632 15.774 1 27.53 ? PA GSP 190 B 1 HETATM 10 O O1A GSP . . . E 2 76.985 33.523 15.978 1 28.54 ? O1A GSP 190 B 1 HETATM 11 O O2A GSP . . . E 2 74.67 34.335 16.257 1 26.98 ? O2A GSP 190 B 1 HETATM 12 O O3A GSP . . . E 2 76.593 36.021 16.328 1 28.15 ? O3A GSP 190 B 1 HETATM 13 O O5' GSP . . . E 2 76.009 35.017 14.202 1 29.21 ? O5' GSP 190 B 1 HETATM 14 C C5' GSP . . . E 2 74.987 35.806 13.611 1 27.97 ? C5' GSP 190 B 1 HETATM 15 C C4' GSP . . . E 2 74.651 35.39 12.171 1 27.86 ? C4' GSP 190 B 1 HETATM 16 O O4' GSP . . . E 2 75.734 35.735 11.33 1 28.75 ? O4' GSP 190 B 1 HETATM 17 C C3' GSP . . . E 2 74.391 33.909 11.933 1 27.54 ? C3' GSP 190 B 1 HETATM 18 O O3' GSP . . . E 2 73.391 33.762 10.952 1 24.38 ? O3' GSP 190 B 1 HETATM 19 C C2' GSP . . . E 2 75.736 33.455 11.394 1 28.78 ? C2' GSP 190 B 1 HETATM 20 O O2' GSP . . . E 2 75.739 32.255 10.65 1 30.75 ? O2' GSP 190 B 1 HETATM 21 C C1' GSP . . . E 2 76.169 34.642 10.577 1 29.65 ? C1' GSP 190 B 1 HETATM 22 N N9 GSP . . . E 2 77.627 34.696 10.455 1 31.08 ? N9 GSP 190 B 1 HETATM 23 C C8 GSP . . . E 2 78.577 34.585 11.434 1 31.77 ? C8 GSP 190 B 1 HETATM 24 N N7 GSP . . . E 2 79.802 34.684 10.867 1 31.57 ? N7 GSP 190 B 1 HETATM 25 C C5 GSP . . . E 2 79.645 34.856 9.539 1 31.51 ? C5 GSP 190 B 1 HETATM 26 C C6 GSP . . . E 2 80.536 35.032 8.496 1 30.88 ? C6 GSP 190 B 1 HETATM 27 O O6 GSP . . . E 2 81.75 35.034 8.699 1 31.15 ? O6 GSP 190 B 1 HETATM 28 N N1 GSP . . . E 2 80.037 35.195 7.229 1 31.14 ? N1 GSP 190 B 1 HETATM 29 C C2 GSP . . . E 2 78.682 35.193 7 1 30.68 ? C2 GSP 190 B 1 HETATM 30 N N2 GSP . . . E 2 78.168 35.349 5.792 1 31.62 ? N2 GSP 190 B 1 HETATM 31 N N3 GSP . . . E 2 77.821 35.023 8.027 1 31.39 ? N3 GSP 190 B 1 HETATM 32 C C4 GSP . . . E 2 78.289 34.872 9.277 1 31.71 ? C4 GSP 190 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #