data_2J5X # _model_server_result.job_id ugd7CjPvyyFIUpA45n2Jnw _model_server_result.datetime_utc '2024-11-22 22:06:05' _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":"C","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 . . . C 2 76.748 29.415 36.451 1 30.87 ? PG GSP 190 A 1 HETATM 2 O O3B GSP . . . C 2 75.949 28.693 35.273 1 32.36 ? O3B GSP 190 A 1 HETATM 3 S S1G GSP . . . C 2 78.356 29.766 35.909 1 28.95 ? S1G GSP 190 A 1 HETATM 4 O O2G GSP . . . C 2 76.757 28.396 37.597 1 31.87 ? O2G GSP 190 A 1 HETATM 5 O O3G GSP . . . C 2 76.069 30.705 36.922 1 29.12 ? O3G GSP 190 A 1 HETATM 6 P PB GSP . . . C 2 74.394 28.37 35.38 1 34.94 ? PB GSP 190 A 1 HETATM 7 O O1B GSP . . . C 2 74.208 26.961 35.806 1 34.55 ? O1B GSP 190 A 1 HETATM 8 O O2B GSP . . . C 2 73.71 29.329 36.264 1 35.13 ? O2B GSP 190 A 1 HETATM 9 P PA GSP . . . C 2 72.932 29.591 33.179 1 37.46 ? PA GSP 190 A 1 HETATM 10 O O1A GSP . . . C 2 71.534 29.378 33.624 1 35.84 ? O1A GSP 190 A 1 HETATM 11 O O2A GSP . . . C 2 73.349 31.01 33.374 1 37.56 ? O2A GSP 190 A 1 HETATM 12 O O3A GSP . . . C 2 73.961 28.526 33.829 1 35.21 ? O3A GSP 190 A 1 HETATM 13 O O5' GSP . . . C 2 73.004 29.135 31.633 1 36.21 ? O5' GSP 190 A 1 HETATM 14 C C5' GSP . . . C 2 73.978 29.606 30.748 1 39.28 ? C5' GSP 190 A 1 HETATM 15 C C4' GSP . . . C 2 73.433 29.771 29.328 1 41.55 ? C4' GSP 190 A 1 HETATM 16 O O4' GSP . . . C 2 72.894 28.563 28.823 1 42.7 ? O4' GSP 190 A 1 HETATM 17 C C3' GSP . . . C 2 72.363 30.845 29.226 1 42.11 ? C3' GSP 190 A 1 HETATM 18 O O3' GSP . . . C 2 72.69 31.69 28.149 1 41.75 ? O3' GSP 190 A 1 HETATM 19 C C2' GSP . . . C 2 71.094 30.067 28.944 1 43.68 ? C2' GSP 190 A 1 HETATM 20 O O2' GSP . . . C 2 70.185 30.764 28.126 1 44.79 ? O2' GSP 190 A 1 HETATM 21 C C1' GSP . . . C 2 71.611 28.802 28.275 1 44.91 ? C1' GSP 190 A 1 HETATM 22 N N9 GSP . . . C 2 70.722 27.663 28.542 1 45.63 ? N9 GSP 190 A 1 HETATM 23 C C8 GSP . . . C 2 70.252 27.254 29.767 1 45.79 ? C8 GSP 190 A 1 HETATM 24 N N7 GSP . . . C 2 69.468 26.171 29.591 1 47.11 ? N7 GSP 190 A 1 HETATM 25 C C5 GSP . . . C 2 69.427 25.864 28.253 1 48.29 ? C5 GSP 190 A 1 HETATM 26 C C6 GSP . . . C 2 68.779 24.855 27.498 1 47.04 ? C6 GSP 190 A 1 HETATM 27 O O6 GSP . . . C 2 68.056 23.982 28.008 1 45.27 ? O6 GSP 190 A 1 HETATM 28 N N1 GSP . . . C 2 68.966 24.847 26.125 1 46.94 ? N1 GSP 190 A 1 HETATM 29 C C2 GSP . . . C 2 69.762 25.789 25.494 1 46.21 ? C2 GSP 190 A 1 HETATM 30 N N2 GSP . . . C 2 69.908 25.754 24.164 1 46 ? N2 GSP 190 A 1 HETATM 31 N N3 GSP . . . C 2 70.391 26.759 26.244 1 45.43 ? N3 GSP 190 A 1 HETATM 32 C C4 GSP . . . C 2 70.223 26.812 27.586 1 47.09 ? C4 GSP 190 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #