data_8VGA # _model_server_result.job_id Y3FbRDqSJcOOdvOOb_Y9pg _model_server_result.datetime_utc '2024-11-06 08:38:22' _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 8vga # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 8VGA # _exptl.entry_id 8VGA _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 115.23 _cell.angle_gamma 90 _cell.entry_id 8VGA _cell.length_a 109.055 _cell.length_b 61.468 _cell.length_c 111.871 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VGA _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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 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 51 A SER 51 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc2 A OG1 THR 191 A THR 191 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc3 C MG MG . A MG 401 1_555 D O3G GSP . A GSP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc4 C MG MG . A MG 401 1_555 D O2B GSP . A GSP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc5 C MG MG . A MG 401 1_555 G O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc6 C MG MG . A MG 401 1_555 G O HOH . A HOH 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc7 B OG SER 51 B SER 51 1_555 E MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc8 B OG1 THR 191 B THR 191 1_555 E MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc9 E MG MG . B MG 401 1_555 F O3G GSP . B GSP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc10 E MG MG . B MG 401 1_555 F O2B GSP . B GSP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc11 E MG MG . B MG 401 1_555 H O HOH . B HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc12 E MG MG . B MG 401 1_555 H O HOH . B HOH 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? # _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 8VGA _atom_sites.fract_transf_matrix[1][1] 0.00917 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004321 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016269 _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] 0.009882 _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 1 401 1381 MG MG . D 3 GSP A 1 402 1382 GSP GSP . E 2 MG B 1 401 1381 MG MG . F 3 GSP B 1 402 1382 GSP GSP . G 4 HOH A 1 501 41 HOH HOH . G 4 HOH A 2 502 120 HOH HOH . G 4 HOH A 3 503 11 HOH HOH . G 4 HOH A 4 504 94 HOH HOH . G 4 HOH A 5 505 2 HOH HOH . G 4 HOH A 6 506 39 HOH HOH . G 4 HOH A 7 507 61 HOH HOH . G 4 HOH A 8 508 133 HOH HOH . G 4 HOH A 9 509 85 HOH HOH . G 4 HOH A 10 510 66 HOH HOH . G 4 HOH A 11 511 67 HOH HOH . G 4 HOH A 12 512 89 HOH HOH . G 4 HOH A 13 513 129 HOH HOH . G 4 HOH A 14 514 24 HOH HOH . G 4 HOH A 15 515 76 HOH HOH . G 4 HOH A 16 516 6 HOH HOH . G 4 HOH A 17 517 149 HOH HOH . G 4 HOH A 18 518 68 HOH HOH . G 4 HOH A 19 519 119 HOH HOH . G 4 HOH A 20 520 146 HOH HOH . G 4 HOH A 21 521 122 HOH HOH . G 4 HOH A 22 522 88 HOH HOH . G 4 HOH A 23 523 91 HOH HOH . G 4 HOH A 24 524 12 HOH HOH . G 4 HOH A 25 525 14 HOH HOH . G 4 HOH A 26 526 92 HOH HOH . G 4 HOH A 27 527 15 HOH HOH . G 4 HOH A 28 528 13 HOH HOH . G 4 HOH A 29 529 48 HOH HOH . G 4 HOH A 30 530 63 HOH HOH . G 4 HOH A 31 531 59 HOH HOH . G 4 HOH A 32 532 51 HOH HOH . G 4 HOH A 33 533 57 HOH HOH . G 4 HOH A 34 534 5 HOH HOH . G 4 HOH A 35 535 10 HOH HOH . G 4 HOH A 36 536 127 HOH HOH . G 4 HOH A 37 537 81 HOH HOH . G 4 HOH A 38 538 47 HOH HOH . G 4 HOH A 39 539 97 HOH HOH . G 4 HOH A 40 540 145 HOH HOH . G 4 HOH A 41 541 100 HOH HOH . G 4 HOH A 42 542 95 HOH HOH . G 4 HOH A 43 543 104 HOH HOH . G 4 HOH A 44 544 26 HOH HOH . G 4 HOH A 45 545 148 HOH HOH . G 4 HOH A 46 546 28 HOH HOH . G 4 HOH A 47 547 139 HOH HOH . G 4 HOH A 48 548 112 HOH HOH . G 4 HOH A 49 549 90 HOH HOH . G 4 HOH A 50 550 36 HOH HOH . G 4 HOH A 51 551 56 HOH HOH . G 4 HOH A 52 552 64 HOH HOH . G 4 HOH A 53 553 82 HOH HOH . G 4 HOH A 54 554 110 HOH HOH . G 4 HOH A 55 555 144 HOH HOH . G 4 HOH A 56 556 135 HOH HOH . G 4 HOH A 57 557 70 HOH HOH . G 4 HOH A 58 558 27 HOH HOH . G 4 HOH A 59 559 69 HOH HOH . G 4 HOH A 60 560 125 HOH HOH . G 4 HOH A 61 561 108 HOH HOH . G 4 HOH A 62 562 35 HOH HOH . G 4 HOH A 63 563 136 HOH HOH . G 4 HOH A 64 564 86 HOH HOH . G 4 HOH A 65 565 140 HOH HOH . G 4 HOH A 66 566 102 HOH HOH . G 4 HOH A 67 567 29 HOH HOH . G 4 HOH A 68 568 130 HOH HOH . G 4 HOH A 69 569 126 HOH HOH . G 4 HOH A 70 570 134 HOH HOH . G 4 HOH A 71 571 131 HOH HOH . G 4 HOH A 72 572 105 HOH HOH . G 4 HOH A 73 573 80 HOH HOH . G 4 HOH A 74 574 99 HOH HOH . G 4 HOH A 75 575 79 HOH HOH . G 4 HOH A 76 576 115 HOH HOH . G 4 HOH A 77 577 138 HOH HOH . G 4 HOH A 78 578 137 HOH HOH . H 4 HOH B 1 501 141 HOH HOH . H 4 HOH B 2 502 143 HOH HOH . H 4 HOH B 3 503 18 HOH HOH . H 4 HOH B 4 504 8 HOH HOH . H 4 HOH B 5 505 20 HOH HOH . H 4 HOH B 6 506 43 HOH HOH . H 4 HOH B 7 507 53 HOH HOH . H 4 HOH B 8 508 71 HOH HOH . H 4 HOH B 9 509 117 HOH HOH . H 4 HOH B 10 510 114 HOH HOH . H 4 HOH B 11 511 107 HOH HOH . H 4 HOH B 12 512 55 HOH HOH . H 4 HOH B 13 513 3 HOH HOH . H 4 HOH B 14 514 34 HOH HOH . H 4 HOH B 15 515 113 HOH HOH . H 4 HOH B 16 516 33 HOH HOH . H 4 HOH B 17 517 87 HOH HOH . H 4 HOH B 18 518 38 HOH HOH . H 4 HOH B 19 519 49 HOH HOH . H 4 HOH B 20 520 22 HOH HOH . H 4 HOH B 21 521 75 HOH HOH . H 4 HOH B 22 522 58 HOH HOH . H 4 HOH B 23 523 1 HOH HOH . H 4 HOH B 24 524 73 HOH HOH . H 4 HOH B 25 525 60 HOH HOH . H 4 HOH B 26 526 109 HOH HOH . H 4 HOH B 27 527 7 HOH HOH . H 4 HOH B 28 528 83 HOH HOH . H 4 HOH B 29 529 54 HOH HOH . H 4 HOH B 30 530 93 HOH HOH . H 4 HOH B 31 531 4 HOH HOH . H 4 HOH B 32 532 30 HOH HOH . H 4 HOH B 33 533 31 HOH HOH . H 4 HOH B 34 534 116 HOH HOH . H 4 HOH B 35 535 101 HOH HOH . H 4 HOH B 36 536 121 HOH HOH . H 4 HOH B 37 537 40 HOH HOH . H 4 HOH B 38 538 21 HOH HOH . H 4 HOH B 39 539 72 HOH HOH . H 4 HOH B 40 540 147 HOH HOH . H 4 HOH B 41 541 23 HOH HOH . H 4 HOH B 42 542 16 HOH HOH . H 4 HOH B 43 543 45 HOH HOH . H 4 HOH B 44 544 32 HOH HOH . H 4 HOH B 45 545 25 HOH HOH . H 4 HOH B 46 546 50 HOH HOH . H 4 HOH B 47 547 98 HOH HOH . H 4 HOH B 48 548 19 HOH HOH . H 4 HOH B 49 549 37 HOH HOH . H 4 HOH B 50 550 17 HOH HOH . H 4 HOH B 51 551 44 HOH HOH . H 4 HOH B 52 552 9 HOH HOH . H 4 HOH B 53 553 96 HOH HOH . H 4 HOH B 54 554 62 HOH HOH . H 4 HOH B 55 555 42 HOH HOH . H 4 HOH B 56 556 77 HOH HOH . H 4 HOH B 57 557 103 HOH HOH . H 4 HOH B 58 558 78 HOH HOH . H 4 HOH B 59 559 123 HOH HOH . H 4 HOH B 60 560 124 HOH HOH . H 4 HOH B 61 561 74 HOH HOH . H 4 HOH B 62 562 128 HOH HOH . H 4 HOH B 63 563 46 HOH HOH . H 4 HOH B 64 564 106 HOH HOH . H 4 HOH B 65 565 111 HOH HOH . H 4 HOH B 66 566 65 HOH HOH . H 4 HOH B 67 567 84 HOH HOH . H 4 HOH B 68 568 142 HOH HOH . H 4 HOH B 69 569 118 HOH HOH . H 4 HOH B 70 570 132 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 . . . F 3 187.469 -16.693 188.754 1 36.71 ? PG GSP 402 B 1 HETATM 2 O O3B GSP . . . F 3 187.451 -15.224 188.074 1 40 ? O3B GSP 402 B 1 HETATM 3 S S1G GSP . . . F 3 187.383 -17.856 187.446 1 43.47 ? S1G GSP 402 B 1 HETATM 4 O O2G GSP . . . F 3 186.281 -16.82 189.729 1 35.8 ? O2G GSP 402 B 1 HETATM 5 O O3G GSP . . . F 3 188.764 -16.802 189.569 1 27.85 ? O3G GSP 402 B 1 HETATM 6 P PB GSP . . . F 3 187.806 -13.853 188.837 1 37.98 ? PB GSP 402 B 1 HETATM 7 O O1B GSP . . . F 3 186.551 -13.277 189.414 1 36.45 ? O1B GSP 402 B 1 HETATM 8 O O2B GSP . . . F 3 188.907 -14.049 189.807 1 31.9 ? O2B GSP 402 B 1 HETATM 9 P PA GSP . . . F 3 189.675 -12.252 187.419 1 41.03 ? PA GSP 402 B 1 HETATM 10 O O1A GSP . . . F 3 190.12 -11.42 188.577 1 40.06 ? O1A GSP 402 B 1 HETATM 11 O O2A GSP . . . F 3 190.648 -13.343 187.143 1 36.21 ? O2A GSP 402 B 1 HETATM 12 O O3A GSP . . . F 3 188.201 -12.826 187.653 1 39.18 ? O3A GSP 402 B 1 HETATM 13 O O5' GSP . . . F 3 189.397 -11.323 186.142 1 46.94 ? O5' GSP 402 B 1 HETATM 14 C C5' GSP . . . F 3 189.309 -11.885 184.858 1 44.26 ? C5' GSP 402 B 1 HETATM 15 C C4' GSP . . . F 3 190.056 -11.015 183.854 1 39.08 ? C4' GSP 402 B 1 HETATM 16 O O4' GSP . . . F 3 189.376 -9.797 183.698 1 41.85 ? O4' GSP 402 B 1 HETATM 17 C C3' GSP . . . F 3 191.481 -10.686 184.244 1 40.99 ? C3' GSP 402 B 1 HETATM 18 O O3' GSP . . . F 3 192.238 -10.739 183.056 1 49.24 ? O3' GSP 402 B 1 HETATM 19 C C2' GSP . . . F 3 191.449 -9.238 184.632 1 43.51 ? C2' GSP 402 B 1 HETATM 20 O O2' GSP . . . F 3 192.583 -8.609 184.094 1 47.42 ? O2' GSP 402 B 1 HETATM 21 C C1' GSP . . . F 3 190.231 -8.704 183.913 1 42.87 ? C1' GSP 402 B 1 HETATM 22 N N9 GSP . . . F 3 189.572 -7.654 184.708 1 45.9 ? N9 GSP 402 B 1 HETATM 23 C C8 GSP . . . F 3 189.271 -7.696 186.038 1 43.8 ? C8 GSP 402 B 1 HETATM 24 N N7 GSP . . . F 3 188.69 -6.518 186.375 1 45.58 ? N7 GSP 402 B 1 HETATM 25 C C5 GSP . . . F 3 188.601 -5.727 185.289 1 49.54 ? C5 GSP 402 B 1 HETATM 26 C C6 GSP . . . F 3 188.092 -4.439 185.074 1 49.05 ? C6 GSP 402 B 1 HETATM 27 O O6 GSP . . . F 3 187.577 -3.775 185.975 1 42.68 ? O6 GSP 402 B 1 HETATM 28 N N1 GSP . . . F 3 188.162 -3.904 183.809 1 51.54 ? N1 GSP 402 B 1 HETATM 29 C C2 GSP . . . F 3 188.724 -4.625 182.782 1 50.4 ? C2 GSP 402 B 1 HETATM 30 N N2 GSP . . . F 3 188.793 -4.096 181.574 1 51.01 ? N2 GSP 402 B 1 HETATM 31 N N3 GSP . . . F 3 189.22 -5.89 182.998 1 51.4 ? N3 GSP 402 B 1 HETATM 32 C C4 GSP . . . F 3 189.161 -6.437 184.231 1 49.48 ? C4 GSP 402 B 1 # _model_server_stats.io_time_ms 88 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 32 #