data_8F0M # _model_server_result.job_id 2rFb1RnOfcZLoDQeINOLQQ _model_server_result.datetime_utc '2025-07-31 17:23:34' _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 8f0m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":202}' # _entry.id 8F0M # _exptl.entry_id 8F0M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 6 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 8F0M _cell.length_a 151.386 _cell.length_b 44.733 _cell.length_c 88.162 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8F0M _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 2 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA 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,B,E,F,G,H,K,L 1 1 C,D,I,J,M,N 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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 O GLY 1 A GLY -1 1_555 I MG MG . C MG 201 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc2 A OG SER 19 A SER 17 1_555 E MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc3 E MG MG . A MG 201 1_555 F O2B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc4 E MG MG . A MG 201 1_555 K O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc5 E MG MG . A MG 201 1_555 K O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc6 E MG MG . A MG 201 1_555 K O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc7 E MG MG . A MG 201 1_555 K O HOH . A HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc8 C OG SER 19 C SER 17 1_555 I MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc9 I MG MG . C MG 201 1_555 J O3G GSP . C GSP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc10 I MG MG . C MG 201 1_555 J O1B GSP . C GSP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc11 I MG MG . C MG 201 1_555 M O HOH . C HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc12 I MG MG . C MG 201 1_555 M O HOH . C HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? # _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 198 n n PG S1G GSP doub 199 n n PG O2G GSP sing 200 n n PG O3G GSP sing 201 n n O3B PB GSP sing 202 n n O2G HOG2 GSP sing 203 n n O3G HOG3 GSP sing 204 n n PB O1B GSP doub 205 n n PB O2B GSP sing 206 n n PB O3A GSP sing 207 n n O2B HOB2 GSP sing 208 n n PA O1A GSP doub 209 n n PA O2A GSP sing 210 n n PA O3A GSP sing 211 n n PA O5' GSP sing 212 n n O2A HOA2 GSP sing 213 n n O5' C5' GSP sing 214 n n C5' C4' GSP sing 215 n n C5' "H5'1" GSP sing 216 n n C5' "H5'2" GSP sing 217 n n C4' O4' GSP sing 218 n n C4' C3' GSP sing 219 n n C4' H4' GSP sing 220 n n O4' C1' GSP sing 221 n n C3' O3' GSP sing 222 n n C3' C2' GSP sing 223 n n C3' H3' GSP sing 224 n n O3' HO3' GSP sing 225 n n C2' O2' GSP sing 226 n n C2' C1' GSP sing 227 n n C2' H2' GSP sing 228 n n O2' HO2' GSP sing 229 n n C1' N9 GSP sing 230 n n C1' H1' GSP sing 231 n n N9 C8 GSP sing 232 n y N9 C4 GSP sing 233 n y C8 N7 GSP doub 234 n y C8 H8 GSP sing 235 n n N7 C5 GSP sing 236 n y C5 C6 GSP sing 237 n n C5 C4 GSP doub 238 n y C6 O6 GSP doub 239 n n C6 N1 GSP sing 240 n n N1 C2 GSP sing 241 n n N1 HN1 GSP sing 242 n n C2 N2 GSP sing 243 n n C2 N3 GSP doub 244 n n N2 HN21 GSP sing 245 n n N2 HN22 GSP sing 246 n n N3 C4 GSP sing 247 n n # _atom_sites.entry_id 8F0M _atom_sites.fract_transf_matrix[1][1] 0.006606 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022355 _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] 0.011343 _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 3 MG A 1 201 201 MG MG . F 4 GDP A 1 202 202 GDP GDP . G 5 GLC A 1 203 202 GLC GLC . H 5 GLC B 1 201 201 GLC GLC . I 3 MG C 1 201 201 MG MG . J 6 GSP C 1 202 202 GSP GSP . K 7 HOH A 1 301 98 HOH HOH . K 7 HOH A 2 302 37 HOH HOH . K 7 HOH A 3 303 97 HOH HOH . K 7 HOH A 4 304 83 HOH HOH . K 7 HOH A 5 305 1 HOH HOH . K 7 HOH A 6 306 26 HOH HOH . K 7 HOH A 7 307 43 HOH HOH . K 7 HOH A 8 308 36 HOH HOH . K 7 HOH A 9 309 7 HOH HOH . K 7 HOH A 10 310 40 HOH HOH . K 7 HOH A 11 311 30 HOH HOH . K 7 HOH A 12 312 3 HOH HOH . K 7 HOH A 13 313 58 HOH HOH . K 7 HOH A 14 314 57 HOH HOH . K 7 HOH A 15 315 48 HOH HOH . K 7 HOH A 16 316 94 HOH HOH . K 7 HOH A 17 317 89 HOH HOH . K 7 HOH A 18 318 19 HOH HOH . K 7 HOH A 19 319 50 HOH HOH . K 7 HOH A 20 320 49 HOH HOH . K 7 HOH A 21 321 4 HOH HOH . K 7 HOH A 22 322 41 HOH HOH . K 7 HOH A 23 323 62 HOH HOH . K 7 HOH A 24 324 92 HOH HOH . K 7 HOH A 25 325 84 HOH HOH . K 7 HOH A 26 326 20 HOH HOH . K 7 HOH A 27 327 71 HOH HOH . K 7 HOH A 28 328 12 HOH HOH . K 7 HOH A 29 329 77 HOH HOH . K 7 HOH A 30 330 21 HOH HOH . K 7 HOH A 31 331 102 HOH HOH . K 7 HOH A 32 332 64 HOH HOH . L 7 HOH B 1 301 23 HOH HOH . L 7 HOH B 2 302 39 HOH HOH . L 7 HOH B 3 303 72 HOH HOH . L 7 HOH B 4 304 68 HOH HOH . L 7 HOH B 5 305 63 HOH HOH . L 7 HOH B 6 306 74 HOH HOH . L 7 HOH B 7 307 70 HOH HOH . L 7 HOH B 8 308 75 HOH HOH . L 7 HOH B 9 309 22 HOH HOH . L 7 HOH B 10 310 88 HOH HOH . L 7 HOH B 11 311 17 HOH HOH . L 7 HOH B 12 312 10 HOH HOH . L 7 HOH B 13 313 53 HOH HOH . L 7 HOH B 14 314 47 HOH HOH . L 7 HOH B 15 315 25 HOH HOH . L 7 HOH B 16 316 69 HOH HOH . L 7 HOH B 17 317 29 HOH HOH . L 7 HOH B 18 318 8 HOH HOH . L 7 HOH B 19 319 9 HOH HOH . L 7 HOH B 20 320 34 HOH HOH . L 7 HOH B 21 321 76 HOH HOH . L 7 HOH B 22 322 80 HOH HOH . L 7 HOH B 23 323 67 HOH HOH . L 7 HOH B 24 324 24 HOH HOH . L 7 HOH B 25 325 28 HOH HOH . L 7 HOH B 26 326 85 HOH HOH . M 7 HOH C 1 301 35 HOH HOH . M 7 HOH C 2 302 55 HOH HOH . M 7 HOH C 3 303 38 HOH HOH . M 7 HOH C 4 304 15 HOH HOH . M 7 HOH C 5 305 13 HOH HOH . M 7 HOH C 6 306 42 HOH HOH . M 7 HOH C 7 307 91 HOH HOH . M 7 HOH C 8 308 27 HOH HOH . M 7 HOH C 9 309 99 HOH HOH . M 7 HOH C 10 310 5 HOH HOH . M 7 HOH C 11 311 61 HOH HOH . M 7 HOH C 12 312 14 HOH HOH . M 7 HOH C 13 313 6 HOH HOH . M 7 HOH C 14 314 60 HOH HOH . M 7 HOH C 15 315 73 HOH HOH . M 7 HOH C 16 316 95 HOH HOH . M 7 HOH C 17 317 65 HOH HOH . M 7 HOH C 18 318 96 HOH HOH . M 7 HOH C 19 319 101 HOH HOH . M 7 HOH C 20 320 46 HOH HOH . M 7 HOH C 21 321 51 HOH HOH . M 7 HOH C 22 322 45 HOH HOH . M 7 HOH C 23 323 56 HOH HOH . M 7 HOH C 24 324 31 HOH HOH . M 7 HOH C 25 325 33 HOH HOH . M 7 HOH C 26 326 44 HOH HOH . M 7 HOH C 27 327 86 HOH HOH . M 7 HOH C 28 328 87 HOH HOH . N 7 HOH D 1 101 11 HOH HOH . N 7 HOH D 2 102 32 HOH HOH . N 7 HOH D 3 103 59 HOH HOH . N 7 HOH D 4 104 54 HOH HOH . N 7 HOH D 5 105 82 HOH HOH . N 7 HOH D 6 106 52 HOH HOH . N 7 HOH D 7 107 2 HOH HOH . N 7 HOH D 8 108 93 HOH HOH . N 7 HOH D 9 109 18 HOH HOH . N 7 HOH D 10 110 79 HOH HOH . N 7 HOH D 11 111 16 HOH HOH . N 7 HOH D 12 112 81 HOH HOH . N 7 HOH D 13 113 100 HOH HOH . N 7 HOH D 14 114 78 HOH HOH . N 7 HOH D 15 115 90 HOH HOH . N 7 HOH D 16 116 66 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 . . . J 6 17.648 27.797 59.074 1 51.35 ? PG GSP 202 C 1 HETATM 2 O O3B GSP . . . J 6 18.297 28.771 60.179 1 43.46 ? O3B GSP 202 C 1 HETATM 3 S S1G GSP . . . J 6 18.731 27.632 57.772 1 56.05 ? S1G GSP 202 C 1 HETATM 4 O O2G GSP . . . J 6 17.361 26.423 59.707 1 49.1 ? O2G GSP 202 C 1 HETATM 5 O O3G GSP . . . J 6 16.321 28.39 58.568 1 33.15 ? O3G GSP 202 C 1 HETATM 6 P PB GSP . . . J 6 17.83 30.302 60.351 1 38.9 ? PB GSP 202 C 1 HETATM 7 O O1B GSP . . . J 6 16.415 30.469 59.959 1 44.18 ? O1B GSP 202 C 1 HETATM 8 O O2B GSP . . . J 6 18.714 31.209 59.585 1 43.83 ? O2B GSP 202 C 1 HETATM 9 P PA GSP . . . J 6 16.746 30.508 62.934 1 38.51 ? PA GSP 202 C 1 HETATM 10 O O1A GSP . . . J 6 15.939 29.291 62.693 1 34.17 ? O1A GSP 202 C 1 HETATM 11 O O2A GSP . . . J 6 15.924 31.736 62.843 1 34.66 ? O2A GSP 202 C 1 HETATM 12 O O3A GSP . . . J 6 17.997 30.57 61.924 1 40.29 ? O3A GSP 202 C 1 HETATM 13 O O5' GSP . . . J 6 17.501 30.414 64.349 1 46.84 ? O5' GSP 202 C 1 HETATM 14 C C5' GSP . . . J 6 18.181 29.231 64.706 1 46.6 ? C5' GSP 202 C 1 HETATM 15 C C4' GSP . . . J 6 18.235 29.129 66.222 1 46.91 ? C4' GSP 202 C 1 HETATM 16 O O4' GSP . . . J 6 18.971 30.227 66.725 1 44.77 ? O4' GSP 202 C 1 HETATM 17 C C3' GSP . . . J 6 16.843 29.193 66.826 1 51.05 ? C3' GSP 202 C 1 HETATM 18 O O3' GSP . . . J 6 16.732 28.213 67.831 1 52.77 ? O3' GSP 202 C 1 HETATM 19 C C2' GSP . . . J 6 16.752 30.57 67.445 1 45.87 ? C2' GSP 202 C 1 HETATM 20 O O2' GSP . . . J 6 16.071 30.514 68.676 1 60.85 ? O2' GSP 202 C 1 HETATM 21 C C1' GSP . . . J 6 18.203 30.967 67.654 1 46.71 ? C1' GSP 202 C 1 HETATM 22 N N9 GSP . . . J 6 18.394 32.416 67.454 1 44.01 ? N9 GSP 202 C 1 HETATM 23 C C8 GSP . . . J 6 18.075 33.156 66.344 1 38.87 ? C8 GSP 202 C 1 HETATM 24 N N7 GSP . . . J 6 18.417 34.446 66.578 1 38.26 ? N7 GSP 202 C 1 HETATM 25 C C5 GSP . . . J 6 18.949 34.536 67.818 1 46.49 ? C5 GSP 202 C 1 HETATM 26 C C6 GSP . . . J 6 19.457 35.601 68.553 1 44.6 ? C6 GSP 202 C 1 HETATM 27 O O6 GSP . . . J 6 19.474 36.734 68.073 1 41 ? O6 GSP 202 C 1 HETATM 28 N N1 GSP . . . J 6 19.943 35.381 69.826 1 47.42 ? N1 GSP 202 C 1 HETATM 29 C C2 GSP . . . J 6 19.924 34.109 70.362 1 56.41 ? C2 GSP 202 C 1 HETATM 30 N N2 GSP . . . J 6 20.391 33.892 71.588 1 50.49 ? N2 GSP 202 C 1 HETATM 31 N N3 GSP . . . J 6 19.418 33.058 69.626 1 45.88 ? N3 GSP 202 C 1 HETATM 32 C C4 GSP . . . J 6 18.94 33.267 68.377 1 47.03 ? C4 GSP 202 C 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 76 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 776 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 32 #