data_5VPZ # _model_server_result.job_id HOoGSKeTwTmRehQO7EPUjA _model_server_result.datetime_utc '2024-11-25 15:07:55' _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 5vpz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 5VPZ # _exptl.entry_id 5VPZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 3 _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 5VPZ _cell.length_a 94.937 _cell.length_b 94.937 _cell.length_c 121.016 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VPZ _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 ? 3 D N N ? 3 F 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 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc2 C MG MG . A MG 201 1_555 D O3G GSP . A GSP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc3 C MG MG . A MG 201 1_555 D O1B GSP . A GSP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc4 C MG MG . A MG 201 1_555 G O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc5 C MG MG . A MG 201 1_555 G O HOH . A HOH 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc6 B OG SER 18 B SER 17 1_555 E MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc7 E MG MG . B MG 201 1_555 F O2G GSP . B GSP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc8 E MG MG . B MG 201 1_555 F O2B GSP . B GSP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc9 E MG MG . B MG 201 1_555 H O HOH . B HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc10 E MG MG . B MG 201 1_555 H O HOH . B HOH 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? # _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 5VPZ _atom_sites.fract_transf_matrix[1][1] 0.010533 _atom_sites.fract_transf_matrix[1][2] 0.006081 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012163 _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] 0.008263 _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 MG A 1 201 1 MG MG . D 3 GSP A 1 202 2 GSP GRS . E 2 MG B 1 201 2 MG MG . F 3 GSP B 1 202 1 GSP GRS . G 4 HOH A 1 301 83 HOH HOH . G 4 HOH A 2 302 57 HOH HOH . G 4 HOH A 3 303 88 HOH HOH . G 4 HOH A 4 304 80 HOH HOH . G 4 HOH A 5 305 45 HOH HOH . G 4 HOH A 6 306 52 HOH HOH . G 4 HOH A 7 307 84 HOH HOH . G 4 HOH A 8 308 82 HOH HOH . G 4 HOH A 9 309 117 HOH HOH . G 4 HOH A 10 310 81 HOH HOH . G 4 HOH A 11 311 18 HOH HOH . G 4 HOH A 12 312 85 HOH HOH . G 4 HOH A 13 313 21 HOH HOH . G 4 HOH A 14 314 89 HOH HOH . G 4 HOH A 15 315 16 HOH HOH . G 4 HOH A 16 316 113 HOH HOH . G 4 HOH A 17 317 60 HOH HOH . G 4 HOH A 18 318 25 HOH HOH . G 4 HOH A 19 319 72 HOH HOH . G 4 HOH A 20 320 59 HOH HOH . G 4 HOH A 21 321 114 HOH HOH . G 4 HOH A 22 322 69 HOH HOH . G 4 HOH A 23 323 30 HOH HOH . G 4 HOH A 24 324 116 HOH HOH . G 4 HOH A 25 325 75 HOH HOH . G 4 HOH A 26 326 6 HOH HOH . G 4 HOH A 27 327 37 HOH HOH . G 4 HOH A 28 328 54 HOH HOH . G 4 HOH A 29 329 22 HOH HOH . G 4 HOH A 30 330 35 HOH HOH . G 4 HOH A 31 331 91 HOH HOH . G 4 HOH A 32 332 26 HOH HOH . G 4 HOH A 33 333 9 HOH HOH . G 4 HOH A 34 334 1 HOH HOH . G 4 HOH A 35 335 12 HOH HOH . G 4 HOH A 36 336 124 HOH HOH . G 4 HOH A 37 337 46 HOH HOH . G 4 HOH A 38 338 111 HOH HOH . G 4 HOH A 39 339 23 HOH HOH . G 4 HOH A 40 340 3 HOH HOH . G 4 HOH A 41 341 17 HOH HOH . G 4 HOH A 42 342 50 HOH HOH . G 4 HOH A 43 343 14 HOH HOH . G 4 HOH A 44 344 10 HOH HOH . G 4 HOH A 45 345 71 HOH HOH . G 4 HOH A 46 346 40 HOH HOH . G 4 HOH A 47 347 62 HOH HOH . G 4 HOH A 48 348 34 HOH HOH . G 4 HOH A 49 349 39 HOH HOH . G 4 HOH A 50 350 44 HOH HOH . G 4 HOH A 51 351 92 HOH HOH . G 4 HOH A 52 352 112 HOH HOH . G 4 HOH A 53 353 13 HOH HOH . G 4 HOH A 54 354 97 HOH HOH . G 4 HOH A 55 355 115 HOH HOH . G 4 HOH A 56 356 79 HOH HOH . G 4 HOH A 57 357 28 HOH HOH . G 4 HOH A 58 358 94 HOH HOH . G 4 HOH A 59 359 86 HOH HOH . G 4 HOH A 60 360 95 HOH HOH . H 4 HOH B 1 301 103 HOH HOH . H 4 HOH B 2 302 104 HOH HOH . H 4 HOH B 3 303 47 HOH HOH . H 4 HOH B 4 304 24 HOH HOH . H 4 HOH B 5 305 36 HOH HOH . H 4 HOH B 6 306 102 HOH HOH . H 4 HOH B 7 307 101 HOH HOH . H 4 HOH B 8 308 106 HOH HOH . H 4 HOH B 9 309 43 HOH HOH . H 4 HOH B 10 310 125 HOH HOH . H 4 HOH B 11 311 99 HOH HOH . H 4 HOH B 12 312 78 HOH HOH . H 4 HOH B 13 313 105 HOH HOH . H 4 HOH B 14 314 41 HOH HOH . H 4 HOH B 15 315 58 HOH HOH . H 4 HOH B 16 316 20 HOH HOH . H 4 HOH B 17 317 38 HOH HOH . H 4 HOH B 18 318 49 HOH HOH . H 4 HOH B 19 319 107 HOH HOH . H 4 HOH B 20 320 63 HOH HOH . H 4 HOH B 21 321 29 HOH HOH . H 4 HOH B 22 322 118 HOH HOH . H 4 HOH B 23 323 64 HOH HOH . H 4 HOH B 24 324 90 HOH HOH . H 4 HOH B 25 325 15 HOH HOH . H 4 HOH B 26 326 5 HOH HOH . H 4 HOH B 27 327 32 HOH HOH . H 4 HOH B 28 328 65 HOH HOH . H 4 HOH B 29 329 67 HOH HOH . H 4 HOH B 30 330 55 HOH HOH . H 4 HOH B 31 331 74 HOH HOH . H 4 HOH B 32 332 122 HOH HOH . H 4 HOH B 33 333 119 HOH HOH . H 4 HOH B 34 334 70 HOH HOH . H 4 HOH B 35 335 4 HOH HOH . H 4 HOH B 36 336 109 HOH HOH . H 4 HOH B 37 337 11 HOH HOH . H 4 HOH B 38 338 77 HOH HOH . H 4 HOH B 39 339 123 HOH HOH . H 4 HOH B 40 340 2 HOH HOH . H 4 HOH B 41 341 68 HOH HOH . H 4 HOH B 42 342 7 HOH HOH . H 4 HOH B 43 343 73 HOH HOH . H 4 HOH B 44 344 56 HOH HOH . H 4 HOH B 45 345 61 HOH HOH . H 4 HOH B 46 346 51 HOH HOH . H 4 HOH B 47 347 27 HOH HOH . H 4 HOH B 48 348 33 HOH HOH . H 4 HOH B 49 349 8 HOH HOH . H 4 HOH B 50 350 96 HOH HOH . H 4 HOH B 51 351 120 HOH HOH . H 4 HOH B 52 352 48 HOH HOH . H 4 HOH B 53 353 53 HOH HOH . H 4 HOH B 54 354 108 HOH HOH . H 4 HOH B 55 355 110 HOH HOH . H 4 HOH B 56 356 66 HOH HOH . H 4 HOH B 57 357 19 HOH HOH . H 4 HOH B 58 358 87 HOH HOH . H 4 HOH B 59 359 42 HOH HOH . H 4 HOH B 60 360 100 HOH HOH . H 4 HOH B 61 361 31 HOH HOH . H 4 HOH B 62 362 93 HOH HOH . H 4 HOH B 63 363 121 HOH HOH . H 4 HOH B 64 364 76 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 . . . D 3 -6.965 -41.484 -21.169 1 52.8 ? PG GSP 202 A 1 HETATM 2 O O3B GSP . . . D 3 -7.658 -41.707 -19.708 1 32.65 ? O3B GSP 202 A 1 HETATM 3 S S1G GSP . . . D 3 -5.059 -41.121 -21.116 1 62.91 ? S1G GSP 202 A 1 HETATM 4 O O2G GSP . . . D 3 -7.334 -42.802 -21.882 1 44 -1 O2G GSP 202 A 1 HETATM 5 O O3G GSP . . . D 3 -7.799 -40.326 -21.681 1 49.15 -1 O3G GSP 202 A 1 HETATM 6 P PB GSP . . . D 3 -8.021 -40.727 -18.495 1 25.18 ? PB GSP 202 A 1 HETATM 7 O O1B GSP . . . D 3 -8.483 -39.424 -18.996 1 23.97 ? O1B GSP 202 A 1 HETATM 8 O O2B GSP . . . D 3 -6.877 -40.743 -17.531 1 25.14 -1 O2B GSP 202 A 1 HETATM 9 P PA GSP . . . D 3 -10.876 -41.08 -17.924 1 27.35 ? PA GSP 202 A 1 HETATM 10 O O1A GSP . . . D 3 -11.309 -41.3 -19.331 1 33.31 -1 O1A GSP 202 A 1 HETATM 11 O O2A GSP . . . D 3 -11.108 -39.724 -17.361 1 24.02 ? O2A GSP 202 A 1 HETATM 12 O O3A GSP . . . D 3 -9.304 -41.448 -17.853 1 24.08 ? O3A GSP 202 A 1 HETATM 13 O O5' GSP . . . D 3 -11.517 -42.169 -16.968 1 28.3 ? O5' GSP 202 A 1 HETATM 14 C C5' GSP . . . D 3 -11.323 -43.573 -17.252 1 30 ? C5' GSP 202 A 1 HETATM 15 C C4' GSP . . . D 3 -12.517 -44.324 -16.726 1 27.53 ? C4' GSP 202 A 1 HETATM 16 O O4' GSP . . . D 3 -12.538 -44.259 -15.273 1 26.12 ? O4' GSP 202 A 1 HETATM 17 C C3' GSP . . . D 3 -13.869 -43.77 -17.191 1 27.92 ? C3' GSP 202 A 1 HETATM 18 O O3' GSP . . . D 3 -14.774 -44.846 -17.407 1 32.32 ? O3' GSP 202 A 1 HETATM 19 C C2' GSP . . . D 3 -14.303 -42.891 -16.019 1 28.33 ? C2' GSP 202 A 1 HETATM 20 O O2' GSP . . . D 3 -15.7 -42.799 -15.889 1 26.98 ? O2' GSP 202 A 1 HETATM 21 C C1' GSP . . . D 3 -13.733 -43.655 -14.828 1 27 ? C1' GSP 202 A 1 HETATM 22 N N9 GSP . . . D 3 -13.423 -42.785 -13.7 1 24.62 ? N9 GSP 202 A 1 HETATM 23 C C8 GSP . . . D 3 -12.632 -41.647 -13.72 1 22.69 ? C8 GSP 202 A 1 HETATM 24 N N7 GSP . . . D 3 -12.497 -41.121 -12.524 1 21.34 ? N7 GSP 202 A 1 HETATM 25 C C5 GSP . . . D 3 -13.268 -41.93 -11.697 1 20.14 ? C5 GSP 202 A 1 HETATM 26 C C6 GSP . . . D 3 -13.484 -41.868 -10.299 1 21.67 ? C6 GSP 202 A 1 HETATM 27 O O6 GSP . . . D 3 -13.022 -41.069 -9.483 1 20.01 ? O6 GSP 202 A 1 HETATM 28 N N1 GSP . . . D 3 -14.331 -42.89 -9.86 1 22.26 ? N1 GSP 202 A 1 HETATM 29 C C2 GSP . . . D 3 -14.879 -43.868 -10.653 1 23.57 ? C2 GSP 202 A 1 HETATM 30 N N2 GSP . . . D 3 -15.664 -44.761 -10.033 1 23.89 ? N2 GSP 202 A 1 HETATM 31 N N3 GSP . . . D 3 -14.624 -43.97 -11.96 1 23.11 ? N3 GSP 202 A 1 HETATM 32 C C4 GSP . . . D 3 -13.85 -42.953 -12.414 1 21.3 ? C4 GSP 202 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 32 #