data_2W2X # _model_server_result.job_id 15gg7LCDFVAvEsc_QLmfGw _model_server_result.datetime_utc '2024-12-20 08:40:24' _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":"G","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 . . . G 4 57.777 -7.628 -20.387 1 61.25 ? PG GSP 1178 B 1 HETATM 2 O O3B GSP . . . G 4 58.419 -8.155 -19.021 1 55.38 ? O3B GSP 1178 B 1 HETATM 3 S S1G GSP . . . G 4 57.794 -8.973 -21.427 1 59.41 ? S1G GSP 1178 B 1 HETATM 4 O O2G GSP . . . G 4 56.35 -7.143 -20.043 1 60.13 ? O2G GSP 1178 B 1 HETATM 5 O O3G GSP . . . G 4 58.56 -6.47 -21.004 1 50.83 ? O3G GSP 1178 B 1 HETATM 6 P PB GSP . . . G 4 59.095 -7.261 -17.87 1 55.81 ? PB GSP 1178 B 1 HETATM 7 O O1B GSP . . . G 4 58.291 -6.108 -17.463 1 35.62 ? O1B GSP 1178 B 1 HETATM 8 O O2B GSP . . . G 4 60.454 -6.791 -18.227 1 60.09 ? O2B GSP 1178 B 1 HETATM 9 P PA GSP . . . G 4 58.223 -8.263 -15.368 1 59.21 ? PA GSP 1178 B 1 HETATM 10 O O1A GSP . . . G 4 56.81 -8.654 -15.567 1 120.8 ? O1A GSP 1178 B 1 HETATM 11 O O2A GSP . . . G 4 58.338 -6.889 -14.819 1 51.45 ? O2A GSP 1178 B 1 HETATM 12 O O3A GSP . . . G 4 59.037 -8.395 -16.75 0.7 32.9 ? O3A GSP 1178 B 1 HETATM 13 O O5' GSP . . . G 4 58.98 -9.331 -14.438 1 66.75 ? O5' GSP 1178 B 1 HETATM 14 C C5' GSP . . . G 4 59.535 -10.492 -15.009 1 45.89 ? C5' GSP 1178 B 1 HETATM 15 C C4' GSP . . . G 4 59.85 -11.513 -13.932 0.7 48.18 ? C4' GSP 1178 B 1 HETATM 16 O O4' GSP . . . G 4 60.966 -11.077 -13.178 0.7 55.22 ? O4' GSP 1178 B 1 HETATM 17 C C3' GSP . . . G 4 58.71 -11.724 -12.944 1 44.09 ? C3' GSP 1178 B 1 HETATM 18 O O3' GSP . . . G 4 58.608 -13.108 -12.755 1 55.75 ? O3' GSP 1178 B 1 HETATM 19 C C2' GSP . . . G 4 59.185 -11.164 -11.622 1 78.72 ? C2' GSP 1178 B 1 HETATM 20 O O2' GSP . . . G 4 58.825 -12.011 -10.538 1 66.71 ? O2' GSP 1178 B 1 HETATM 21 C C1' GSP . . . G 4 60.696 -11.15 -11.791 1 64.9 ? C1' GSP 1178 B 1 HETATM 22 N N9 GSP . . . G 4 61.259 -9.955 -11.18 1 64.61 ? N9 GSP 1178 B 1 HETATM 23 C C8 GSP . . . G 4 61.043 -8.678 -11.619 1 59.52 ? C8 GSP 1178 B 1 HETATM 24 N N7 GSP . . . G 4 61.739 -7.837 -10.825 1 76.52 ? N7 GSP 1178 B 1 HETATM 25 C C5 GSP . . . G 4 62.404 -8.567 -9.892 1 72.61 ? C5 GSP 1178 B 1 HETATM 26 C C6 GSP . . . G 4 63.251 -8.204 -8.85 1 64.31 ? C6 GSP 1178 B 1 HETATM 27 O O6 GSP . . . G 4 63.511 -7.015 -8.654 1 59.8 ? O6 GSP 1178 B 1 HETATM 28 N N1 GSP . . . G 4 63.786 -9.186 -8.035 1 82.67 ? N1 GSP 1178 B 1 HETATM 29 C C2 GSP . . . G 4 63.48 -10.517 -8.265 1 83.31 ? C2 GSP 1178 B 1 HETATM 30 N N2 GSP . . . G 4 63.98 -11.47 -7.48 1 77.06 ? N2 GSP 1178 B 1 HETATM 31 N N3 GSP . . . G 4 62.643 -10.865 -9.309 0.7 97.69 ? N3 GSP 1178 B 1 HETATM 32 C C4 GSP . . . G 4 62.11 -9.909 -10.109 1 75.12 ? C4 GSP 1178 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #