data_5VQ6 # _model_server_result.job_id jNJ2ekGEauVH1xKx2Jw5lQ _model_server_result.datetime_utc '2024-11-22 10:59:02' _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 5vq6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5VQ6 # _exptl.entry_id 5VQ6 _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 120 _cell.entry_id 5VQ6 _cell.length_a 95.117 _cell.length_b 95.117 _cell.length_c 121.417 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VQ6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA 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 OG SER 18 A SER 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc2 C O3G GSP . A GSP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc3 C O1B GSP . A GSP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc4 D MG MG . A MG 202 1_555 G O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc5 D MG MG . A MG 202 1_555 G O HOH . A HOH 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc6 B OG SER 18 B SER 17 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc7 E O3G GSP . B GSP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc8 E O2B GSP . B GSP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc9 F MG MG . B MG 202 1_555 H O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc10 F MG MG . B MG 202 1_555 H O HOH . B HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? # _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 5VQ6 _atom_sites.fract_transf_matrix[1][1] 0.010513 _atom_sites.fract_transf_matrix[1][2] 0.00607 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01214 _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] 0.008236 _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 1 201 1 GSP GRS . D 3 MG A 1 202 2 MG MG . E 2 GSP B 1 201 2 GSP GRS . F 3 MG B 1 202 1 MG MG . G 4 HOH A 1 301 24 HOH HOH . G 4 HOH A 2 302 83 HOH HOH . G 4 HOH A 3 303 27 HOH HOH . G 4 HOH A 4 304 26 HOH HOH . G 4 HOH A 5 305 66 HOH HOH . G 4 HOH A 6 306 81 HOH HOH . G 4 HOH A 7 307 63 HOH HOH . G 4 HOH A 8 308 21 HOH HOH . G 4 HOH A 9 309 46 HOH HOH . G 4 HOH A 10 310 71 HOH HOH . G 4 HOH A 11 311 72 HOH HOH . G 4 HOH A 12 312 29 HOH HOH . G 4 HOH A 13 313 30 HOH HOH . G 4 HOH A 14 314 76 HOH HOH . G 4 HOH A 15 315 77 HOH HOH . G 4 HOH A 16 316 25 HOH HOH . G 4 HOH A 17 317 41 HOH HOH . G 4 HOH A 18 318 3 HOH HOH . G 4 HOH A 19 319 12 HOH HOH . G 4 HOH A 20 320 56 HOH HOH . G 4 HOH A 21 321 73 HOH HOH . G 4 HOH A 22 322 70 HOH HOH . G 4 HOH A 23 323 14 HOH HOH . G 4 HOH A 24 324 74 HOH HOH . G 4 HOH A 25 325 7 HOH HOH . G 4 HOH A 26 326 28 HOH HOH . G 4 HOH A 27 327 1 HOH HOH . G 4 HOH A 28 328 67 HOH HOH . G 4 HOH A 29 329 16 HOH HOH . G 4 HOH A 30 330 44 HOH HOH . G 4 HOH A 31 331 43 HOH HOH . G 4 HOH A 32 332 37 HOH HOH . G 4 HOH A 33 333 13 HOH HOH . G 4 HOH A 34 334 69 HOH HOH . G 4 HOH A 35 335 45 HOH HOH . G 4 HOH A 36 336 42 HOH HOH . G 4 HOH A 37 337 82 HOH HOH . G 4 HOH A 38 338 75 HOH HOH . G 4 HOH A 39 339 68 HOH HOH . G 4 HOH A 40 340 80 HOH HOH . G 4 HOH A 41 341 84 HOH HOH . G 4 HOH A 42 342 87 HOH HOH . G 4 HOH A 43 343 47 HOH HOH . G 4 HOH A 44 344 15 HOH HOH . G 4 HOH A 45 345 38 HOH HOH . H 4 HOH B 1 301 32 HOH HOH . H 4 HOH B 2 302 64 HOH HOH . H 4 HOH B 3 303 59 HOH HOH . H 4 HOH B 4 304 35 HOH HOH . H 4 HOH B 5 305 23 HOH HOH . H 4 HOH B 6 306 17 HOH HOH . H 4 HOH B 7 307 85 HOH HOH . H 4 HOH B 8 308 8 HOH HOH . H 4 HOH B 9 309 22 HOH HOH . H 4 HOH B 10 310 11 HOH HOH . H 4 HOH B 11 311 4 HOH HOH . H 4 HOH B 12 312 49 HOH HOH . H 4 HOH B 13 313 51 HOH HOH . H 4 HOH B 14 314 55 HOH HOH . H 4 HOH B 15 315 31 HOH HOH . H 4 HOH B 16 316 34 HOH HOH . H 4 HOH B 17 317 20 HOH HOH . H 4 HOH B 18 318 62 HOH HOH . H 4 HOH B 19 319 10 HOH HOH . H 4 HOH B 20 320 2 HOH HOH . H 4 HOH B 21 321 53 HOH HOH . H 4 HOH B 22 322 6 HOH HOH . H 4 HOH B 23 323 18 HOH HOH . H 4 HOH B 24 324 19 HOH HOH . H 4 HOH B 25 325 52 HOH HOH . H 4 HOH B 26 326 65 HOH HOH . H 4 HOH B 27 327 5 HOH HOH . H 4 HOH B 28 328 33 HOH HOH . H 4 HOH B 29 329 36 HOH HOH . H 4 HOH B 30 330 54 HOH HOH . H 4 HOH B 31 331 78 HOH HOH . H 4 HOH B 32 332 57 HOH HOH . H 4 HOH B 33 333 48 HOH HOH . H 4 HOH B 34 334 60 HOH HOH . H 4 HOH B 35 335 40 HOH HOH . H 4 HOH B 36 336 61 HOH HOH . H 4 HOH B 37 337 79 HOH HOH . H 4 HOH B 38 338 86 HOH HOH . H 4 HOH B 39 339 88 HOH HOH . H 4 HOH B 40 340 50 HOH HOH . H 4 HOH B 41 341 9 HOH HOH . H 4 HOH B 42 342 39 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 -6.893 -13.321 21.078 1 72.17 ? PG GSP 201 B 1 HETATM 2 O O3B GSP . . . E 2 -7.639 -13.058 19.648 1 36.28 ? O3B GSP 201 B 1 HETATM 3 S S1G GSP . . . E 2 -4.946 -13.535 20.908 1 85.48 ? S1G GSP 201 B 1 HETATM 4 O O2G GSP . . . E 2 -7.327 -12.084 21.855 1 68.11 -1 O2G GSP 201 B 1 HETATM 5 O O3G GSP . . . E 2 -7.604 -14.536 21.648 1 60.72 -1 O3G GSP 201 B 1 HETATM 6 P PB GSP . . . E 2 -8.102 -14.022 18.452 1 22.58 ? PB GSP 201 B 1 HETATM 7 O O1B GSP . . . E 2 -7.024 -14.023 17.41 1 24.02 -1 O1B GSP 201 B 1 HETATM 8 O O2B GSP . . . E 2 -8.562 -15.313 19.021 1 26.19 ? O2B GSP 201 B 1 HETATM 9 P PA GSP . . . E 2 -10.973 -13.634 17.966 1 25.41 ? PA GSP 201 B 1 HETATM 10 O O1A GSP . . . E 2 -11.212 -15.002 17.433 1 24.75 ? O1A GSP 201 B 1 HETATM 11 O O2A GSP . . . E 2 -11.4 -13.35 19.372 1 28.53 -1 O2A GSP 201 B 1 HETATM 12 O O3A GSP . . . E 2 -9.404 -13.296 17.843 1 24.31 ? O3A GSP 201 B 1 HETATM 13 O O5' GSP . . . E 2 -11.628 -12.562 16.986 1 22.96 ? O5' GSP 201 B 1 HETATM 14 C C5' GSP . . . E 2 -11.374 -11.16 17.208 1 24.01 ? C5' GSP 201 B 1 HETATM 15 C C4' GSP . . . E 2 -12.526 -10.352 16.662 1 25.24 ? C4' GSP 201 B 1 HETATM 16 O O4' GSP . . . E 2 -12.534 -10.401 15.207 1 21 ? O4' GSP 201 B 1 HETATM 17 C C3' GSP . . . E 2 -13.915 -10.822 17.116 1 27.42 ? C3' GSP 201 B 1 HETATM 18 O O3' GSP . . . E 2 -14.79 -9.72 17.318 1 30.58 ? O3' GSP 201 B 1 HETATM 19 C C2' GSP . . . E 2 -14.371 -11.692 15.946 1 25.9 ? C2' GSP 201 B 1 HETATM 20 O O2' GSP . . . E 2 -15.77 -11.75 15.79 1 24.75 ? O2' GSP 201 B 1 HETATM 21 C C1' GSP . . . E 2 -13.76 -10.951 14.761 1 24.52 ? C1' GSP 201 B 1 HETATM 22 N N9 GSP . . . E 2 -13.5 -11.853 13.65 1 19.7 ? N9 GSP 201 B 1 HETATM 23 C C8 GSP . . . E 2 -12.785 -13.039 13.715 1 18.81 ? C8 GSP 201 B 1 HETATM 24 N N7 GSP . . . E 2 -12.61 -13.565 12.521 1 19.1 ? N7 GSP 201 B 1 HETATM 25 C C5 GSP . . . E 2 -13.375 -12.767 11.67 1 18.8 ? C5 GSP 201 B 1 HETATM 26 C C6 GSP . . . E 2 -13.617 -12.88 10.276 1 19.24 ? C6 GSP 201 B 1 HETATM 27 O O6 GSP . . . E 2 -13.177 -13.712 9.481 1 15.54 ? O6 GSP 201 B 1 HETATM 28 N N1 GSP . . . E 2 -14.406 -11.833 9.807 1 19.43 ? N1 GSP 201 B 1 HETATM 29 C C2 GSP . . . E 2 -14.941 -10.83 10.58 1 20.07 ? C2 GSP 201 B 1 HETATM 30 N N2 GSP . . . E 2 -15.721 -9.945 9.945 1 20.81 ? N2 GSP 201 B 1 HETATM 31 N N3 GSP . . . E 2 -14.682 -10.693 11.876 1 18.87 ? N3 GSP 201 B 1 HETATM 32 C C4 GSP . . . E 2 -13.923 -11.707 12.357 1 17.84 ? C4 GSP 201 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #