data_2W2X # _model_server_result.job_id rxqrOQ84_RQREX-jj1bJOw _model_server_result.datetime_utc '2024-12-20 08:14:37' _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 2w2x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1178}' # _entry.id 2W2X # _exptl.entry_id 2W2X _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 112.21 _cell.angle_gamma 90 _cell.entry_id 2W2X _cell.length_a 131.57 _cell.length_b 84.459 _cell.length_c 74.196 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2W2X _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 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 PQS dimeric 2 author_and_software_defined_assembly 1 PQS dimeric 2 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,D,E,F,I,L 1 1 B,C,G,H,J,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 G 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 23 A THR 17 1_555 F MG MG . A MG 1179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc2 A OG1 THR 41 A THR 35 1_555 F MG MG . A MG 1179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc3 E O2G GSP . A GSP 1178 1_555 F MG MG . A MG 1179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc4 E O2B GSP . A GSP 1178 1_555 F MG MG . A MG 1179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc5 B OG1 THR 23 B THR 17 1_555 H MG MG . B MG 1179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc6 B OG1 THR 41 B THR 35 1_555 H MG MG . B MG 1179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc7 G O2G GSP . B GSP 1178 1_555 H MG MG . B MG 1179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc8 G O1B GSP . B GSP 1178 1_555 H MG MG . B MG 1179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? # _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 2W2X _atom_sites.fract_transf_matrix[1][1] 0.007601 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003103 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01184 _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] 0.014558 _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 4 GSP A 1 1178 1178 GSP GSP . F 5 MG A 1 1179 1179 MG MG . G 4 GSP B 1 1178 1178 GSP GSP . H 5 MG B 1 1179 1179 MG MG . I 6 HOH A 1 2001 2001 HOH HOH . I 6 HOH A 2 2002 2002 HOH HOH . I 6 HOH A 3 2003 2003 HOH HOH . I 6 HOH A 4 2004 2004 HOH HOH . I 6 HOH A 5 2005 2005 HOH HOH . I 6 HOH A 6 2006 2006 HOH HOH . I 6 HOH A 7 2007 2007 HOH HOH . I 6 HOH A 8 2008 2008 HOH HOH . I 6 HOH A 9 2009 2009 HOH HOH . I 6 HOH A 10 2010 2010 HOH HOH . I 6 HOH A 11 2011 2011 HOH HOH . I 6 HOH A 12 2012 2012 HOH HOH . J 6 HOH B 1 2001 2001 HOH HOH . J 6 HOH B 2 2002 2002 HOH HOH . J 6 HOH B 3 2003 2003 HOH HOH . J 6 HOH B 4 2004 2004 HOH HOH . J 6 HOH B 5 2005 2005 HOH HOH . J 6 HOH B 6 2006 2006 HOH HOH . J 6 HOH B 7 2007 2007 HOH HOH . J 6 HOH B 8 2008 2008 HOH HOH . J 6 HOH B 9 2009 2009 HOH HOH . J 6 HOH B 10 2010 2010 HOH HOH . J 6 HOH B 11 2011 2011 HOH HOH . K 6 HOH C 1 2002 2002 HOH HOH . K 6 HOH C 2 2003 2003 HOH HOH . K 6 HOH C 3 2004 2004 HOH HOH . K 6 HOH C 4 2005 2005 HOH HOH . K 6 HOH C 5 2006 2006 HOH HOH . K 6 HOH C 6 2007 2007 HOH HOH . L 6 HOH D 1 2001 2001 HOH HOH . L 6 HOH D 2 2002 2002 HOH HOH . L 6 HOH D 3 2003 2003 HOH HOH . L 6 HOH D 4 2004 2004 HOH HOH . L 6 HOH D 5 2005 2005 HOH HOH . L 6 HOH D 6 2006 2006 HOH HOH . L 6 HOH D 7 2007 2007 HOH HOH . L 6 HOH D 8 2008 2008 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 4 30.402 12.009 11.517 1 49.98 ? PG GSP 1178 A 1 HETATM 2 O O3B GSP . . . E 4 31.141 12.413 10.146 1 107.85 ? O3B GSP 1178 A 1 HETATM 3 S S1G GSP . . . E 4 30.887 13.069 12.767 1 64.9 ? S1G GSP 1178 A 1 HETATM 4 O O2G GSP . . . E 4 28.892 12.143 11.247 1 69.6 ? O2G GSP 1178 A 1 HETATM 5 O O3G GSP . . . E 4 30.715 10.541 11.861 1 33.02 ? O3G GSP 1178 A 1 HETATM 6 P PB GSP . . . E 4 31.59 11.338 9.039 1 51.83 ? PB GSP 1178 A 1 HETATM 7 O O1B GSP . . . E 4 32.542 10.344 9.562 1 61.75 ? O1B GSP 1178 A 1 HETATM 8 O O2B GSP . . . E 4 30.422 10.631 8.479 1 37.03 ? O2B GSP 1178 A 1 HETATM 9 P PA GSP . . . E 4 31.484 13.061 6.893 1 56.96 ? PA GSP 1178 A 1 HETATM 10 O O1A GSP . . . E 4 31.055 12.039 5.908 1 40.05 ? O1A GSP 1178 A 1 HETATM 11 O O2A GSP . . . E 4 30.337 13.737 7.541 1 81.78 ? O2A GSP 1178 A 1 HETATM 12 O O3A GSP . . . E 4 32.347 12.289 7.999 1 49.61 ? O3A GSP 1178 A 1 HETATM 13 O O5' GSP . . . E 4 32.537 14.077 6.243 1 49.1 ? O5' GSP 1178 A 1 HETATM 14 C C5' GSP . . . E 4 33.194 15.047 7.026 1 41.33 ? C5' GSP 1178 A 1 HETATM 15 C C4' GSP . . . E 4 33.901 16.039 6.098 1 63.5 ? C4' GSP 1178 A 1 HETATM 16 O O4' GSP . . . E 4 34.903 15.378 5.336 1 62.79 ? O4' GSP 1178 A 1 HETATM 17 C C3' GSP . . . E 4 32.917 16.662 5.123 1 71.17 ? C3' GSP 1178 A 1 HETATM 18 O O3' GSP . . . E 4 33.043 18.06 5.142 1 100.13 ? O3' GSP 1178 A 1 HETATM 19 C C2' GSP . . . E 4 33.337 16.181 3.762 1 60.38 ? C2' GSP 1178 A 1 HETATM 20 O O2' GSP . . . E 4 33.326 17.271 2.869 1 91.48 ? O2' GSP 1178 A 1 HETATM 21 C C1' GSP . . . E 4 34.751 15.666 3.962 1 54.25 ? C1' GSP 1178 A 1 HETATM 22 N N9 GSP . . . E 4 34.884 14.456 3.137 1 50.63 ? N9 GSP 1178 A 1 HETATM 23 C C8 GSP . . . E 4 34.157 13.296 3.254 1 54.24 ? C8 GSP 1178 A 1 HETATM 24 N N7 GSP . . . E 4 34.566 12.43 2.292 1 65.01 ? N7 GSP 1178 A 1 HETATM 25 C C5 GSP . . . E 4 35.545 13.036 1.568 1 67.13 ? C5 GSP 1178 A 1 HETATM 26 C C6 GSP . . . E 4 36.3 12.624 0.478 1 57.64 ? C6 GSP 1178 A 1 HETATM 27 O O6 GSP . . . E 4 36.13 11.494 0.004 1 68.6 ? O6 GSP 1178 A 1 HETATM 28 N N1 GSP . . . E 4 37.236 13.481 -0.072 1 46.03 ? N1 GSP 1178 A 1 HETATM 29 C C2 GSP . . . E 4 37.434 14.744 0.45 1 63.87 ? C2 GSP 1178 A 1 HETATM 30 N N2 GSP . . . E 4 38.342 15.56 -0.089 1 43.52 ? N2 GSP 1178 A 1 HETATM 31 N N3 GSP . . . E 4 36.678 15.149 1.534 1 58.17 ? N3 GSP 1178 A 1 HETATM 32 C C4 GSP . . . E 4 35.75 14.312 2.082 1 60.86 ? C4 GSP 1178 A 1 # _model_server_stats.io_time_ms 75 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 32 #