data_5MLA # _model_server_result.job_id 5Y_6INsHYPakqKAZR-GkQg _model_server_result.datetime_utc '2024-11-23 02:45:31' _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 5mla # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 5MLA # _exptl.entry_id 5MLA _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 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 120 _cell.entry_id 5MLA _cell.length_a 112.83 _cell.length_b 112.83 _cell.length_c 66.77 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MLA _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 4 _struct_asym.id D _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 OG SER 20 A SER 17 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc2 A OG1 THR 38 A THR 35 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc3 C MG MG . A MG 201 1_555 D O2B GSP . A GSP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc4 C MG MG . A MG 201 1_555 D O2G GSP . A GSP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc5 C MG MG . A MG 201 1_555 G O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc6 C MG MG . A MG 201 1_555 G O HOH . A HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? # _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 5MLA _atom_sites.fract_transf_matrix[1][1] 0.008863 _atom_sites.fract_transf_matrix[1][2] 0.005117 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010234 _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] 0.014977 _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 3 MG A 1 201 2 MG MG . D 4 GSP A 1 202 1 GSP GSP . E 5 SO4 A 1 203 2 SO4 SO4 . F 5 SO4 B 1 201 1 SO4 SO4 . G 6 HOH A 1 301 73 HOH HOH . G 6 HOH A 2 302 64 HOH HOH . G 6 HOH A 3 303 44 HOH HOH . G 6 HOH A 4 304 52 HOH HOH . G 6 HOH A 5 305 67 HOH HOH . G 6 HOH A 6 306 51 HOH HOH . G 6 HOH A 7 307 48 HOH HOH . G 6 HOH A 8 308 11 HOH HOH . G 6 HOH A 9 309 46 HOH HOH . G 6 HOH A 10 310 41 HOH HOH . G 6 HOH A 11 311 22 HOH HOH . G 6 HOH A 12 312 14 HOH HOH . G 6 HOH A 13 313 16 HOH HOH . G 6 HOH A 14 314 86 HOH HOH . G 6 HOH A 15 315 82 HOH HOH . G 6 HOH A 16 316 10 HOH HOH . G 6 HOH A 17 317 66 HOH HOH . G 6 HOH A 18 318 21 HOH HOH . G 6 HOH A 19 319 12 HOH HOH . G 6 HOH A 20 320 30 HOH HOH . G 6 HOH A 21 321 32 HOH HOH . G 6 HOH A 22 322 23 HOH HOH . G 6 HOH A 23 323 24 HOH HOH . G 6 HOH A 24 324 53 HOH HOH . G 6 HOH A 25 325 9 HOH HOH . G 6 HOH A 26 326 20 HOH HOH . G 6 HOH A 27 327 84 HOH HOH . G 6 HOH A 28 328 34 HOH HOH . G 6 HOH A 29 329 8 HOH HOH . G 6 HOH A 30 330 28 HOH HOH . G 6 HOH A 31 331 13 HOH HOH . G 6 HOH A 32 332 50 HOH HOH . G 6 HOH A 33 333 58 HOH HOH . G 6 HOH A 34 334 87 HOH HOH . G 6 HOH A 35 335 39 HOH HOH . G 6 HOH A 36 336 17 HOH HOH . G 6 HOH A 37 337 68 HOH HOH . G 6 HOH A 38 338 76 HOH HOH . G 6 HOH A 39 339 83 HOH HOH . G 6 HOH A 40 340 55 HOH HOH . G 6 HOH A 41 341 37 HOH HOH . G 6 HOH A 42 342 36 HOH HOH . G 6 HOH A 43 343 4 HOH HOH . G 6 HOH A 44 344 54 HOH HOH . G 6 HOH A 45 345 69 HOH HOH . G 6 HOH A 46 346 65 HOH HOH . G 6 HOH A 47 347 18 HOH HOH . G 6 HOH A 48 348 33 HOH HOH . G 6 HOH A 49 349 88 HOH HOH . G 6 HOH A 50 350 70 HOH HOH . G 6 HOH A 51 351 49 HOH HOH . G 6 HOH A 52 352 90 HOH HOH . G 6 HOH A 53 353 19 HOH HOH . G 6 HOH A 54 354 15 HOH HOH . G 6 HOH A 55 355 45 HOH HOH . G 6 HOH A 56 356 43 HOH HOH . G 6 HOH A 57 357 75 HOH HOH . G 6 HOH A 58 358 35 HOH HOH . G 6 HOH A 59 359 25 HOH HOH . G 6 HOH A 60 360 26 HOH HOH . G 6 HOH A 61 361 47 HOH HOH . G 6 HOH A 62 362 27 HOH HOH . G 6 HOH A 63 363 42 HOH HOH . H 6 HOH B 1 301 72 HOH HOH . H 6 HOH B 2 302 57 HOH HOH . H 6 HOH B 3 303 6 HOH HOH . H 6 HOH B 4 304 78 HOH HOH . H 6 HOH B 5 305 77 HOH HOH . H 6 HOH B 6 306 80 HOH HOH . H 6 HOH B 7 307 60 HOH HOH . H 6 HOH B 8 308 7 HOH HOH . H 6 HOH B 9 309 63 HOH HOH . H 6 HOH B 10 310 31 HOH HOH . H 6 HOH B 11 311 61 HOH HOH . H 6 HOH B 12 312 38 HOH HOH . H 6 HOH B 13 313 62 HOH HOH . H 6 HOH B 14 314 79 HOH HOH . H 6 HOH B 15 315 89 HOH HOH . H 6 HOH B 16 316 74 HOH HOH . H 6 HOH B 17 317 81 HOH HOH . H 6 HOH B 18 318 71 HOH HOH . H 6 HOH B 19 319 91 HOH HOH . H 6 HOH B 20 320 59 HOH HOH . H 6 HOH B 21 321 29 HOH HOH . H 6 HOH B 22 322 85 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 4 69.398 93.154 14.002 1 42.12 ? PG GSP 202 A 1 HETATM 2 O O3B GSP . . . D 4 69.225 92.298 12.602 1 34.73 ? O3B GSP 202 A 1 HETATM 3 S S1G GSP . . . D 4 67.774 92.975 15.094 1 48.72 ? S1G GSP 202 A 1 HETATM 4 O O2G GSP . . . D 4 70.629 92.623 14.884 1 40.59 ? O2G GSP 202 A 1 HETATM 5 O O3G GSP . . . D 4 69.618 94.708 13.668 1 41.53 ? O3G GSP 202 A 1 HETATM 6 P PB GSP . . . D 4 70.411 91.979 11.536 1 28.88 ? PB GSP 202 A 1 HETATM 7 O O1B GSP . . . D 4 70.356 92.926 10.369 1 27.7 ? O1B GSP 202 A 1 HETATM 8 O O2B GSP . . . D 4 71.69 91.87 12.319 1 27.18 ? O2B GSP 202 A 1 HETATM 9 P PA GSP . . . D 4 70.795 89.162 11.043 1 26.98 ? PA GSP 202 A 1 HETATM 10 O O1A GSP . . . D 4 72.173 89.229 10.455 1 29.3 ? O1A GSP 202 A 1 HETATM 11 O O2A GSP . . . D 4 70.624 88.698 12.46 1 26.7 ? O2A GSP 202 A 1 HETATM 12 O O3A GSP . . . D 4 70.014 90.569 10.854 1 29.04 ? O3A GSP 202 A 1 HETATM 13 O O5' GSP . . . D 4 69.979 88.184 10.069 1 28.53 ? O5' GSP 202 A 1 HETATM 14 C C5' GSP . . . D 4 68.612 87.836 10.338 1 27.71 ? C5' GSP 202 A 1 HETATM 15 C C4' GSP . . . D 4 68.235 86.554 9.613 1 26.71 ? C4' GSP 202 A 1 HETATM 16 O O4' GSP . . . D 4 68.425 86.675 8.188 1 26.3 ? O4' GSP 202 A 1 HETATM 17 C C3' GSP . . . D 4 69.088 85.395 10.059 1 27.48 ? C3' GSP 202 A 1 HETATM 18 O O3' GSP . . . D 4 68.289 84.227 10.034 1 30.98 ? O3' GSP 202 A 1 HETATM 19 C C2' GSP . . . D 4 70.122 85.257 8.98 1 27.83 ? C2' GSP 202 A 1 HETATM 20 O O2' GSP . . . D 4 70.608 83.929 8.813 1 29.58 ? O2' GSP 202 A 1 HETATM 21 C C1' GSP . . . D 4 69.336 85.67 7.741 1 27.06 ? C1' GSP 202 A 1 HETATM 22 N N9 GSP . . . D 4 70.229 86.181 6.697 1 26.97 ? N9 GSP 202 A 1 HETATM 23 C C8 GSP . . . D 4 71.186 87.128 6.869 1 27.44 ? C8 GSP 202 A 1 HETATM 24 N N7 GSP . . . D 4 71.836 87.371 5.712 1 28.17 ? N7 GSP 202 A 1 HETATM 25 C C5 GSP . . . D 4 71.282 86.568 4.791 1 27.75 ? C5 GSP 202 A 1 HETATM 26 C C6 GSP . . . D 4 71.493 86.334 3.361 1 27.6 ? C6 GSP 202 A 1 HETATM 27 O O6 GSP . . . D 4 72.362 86.96 2.734 1 27.96 ? O6 GSP 202 A 1 HETATM 28 N N1 GSP . . . D 4 70.731 85.43 2.758 1 28.39 ? N1 GSP 202 A 1 HETATM 29 C C2 GSP . . . D 4 69.777 84.732 3.403 1 27.57 ? C2 GSP 202 A 1 HETATM 30 N N2 GSP . . . D 4 69.05 83.841 2.698 1 27.21 ? N2 GSP 202 A 1 HETATM 31 N N3 GSP . . . D 4 69.519 84.888 4.725 1 27.55 ? N3 GSP 202 A 1 HETATM 32 C C4 GSP . . . D 4 70.228 85.782 5.442 1 26.93 ? C4 GSP 202 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #