data_4DST # _model_server_result.job_id IXYqu6WwkVGyHwYmR7BTow _model_server_result.datetime_utc '2024-11-05 10:34:32' _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 4dst # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 4DST # _exptl.entry_id 4DST _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 521.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _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 4DST _cell.length_a 78.923 _cell.length_b 78.923 _cell.length_c 78.631 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DST _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,I,J _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 3 _struct_asym.id C _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 11 A GLY 10 1_555 I MG MG . A MG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc2 A OG SER 18 A SER 17 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc3 A OG1 THR 36 A THR 35 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc4 A O ALA 60 A ALA 59 1_555 I MG MG . A MG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc5 A O GLY 61 A GLY 60 1_555 I MG MG . A MG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc6 A OH TYR 97 A TYR 96 1_555 I MG MG . A MG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc7 C O2B GCP . A GCP 202 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc8 C O1G GCP . A GCP 202 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc9 D MG MG . A MG 203 1_555 J O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc10 D MG MG . A MG 203 1_555 J O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc11 I MG MG . A MG 208 1_555 J O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc12 I MG MG . A MG 208 1_555 J O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? # _chem_comp.formula 'C11 H18 N5 O13 P3' _chem_comp.formula_weight 521.208 _chem_comp.id GCP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _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 O1G GCP doub 135 n n PG O2G GCP sing 136 n n PG O3G GCP sing 137 n n PG C3B GCP sing 138 n n O2G HOG2 GCP sing 139 n n O3G HOG3 GCP sing 140 n n C3B PB GCP sing 141 n n C3B H3B1 GCP sing 142 n n C3B H3B2 GCP sing 143 n n PB O1B GCP doub 144 n n PB O2B GCP sing 145 n n PB O3A GCP sing 146 n n O2B HOB2 GCP sing 147 n n O3A PA GCP sing 148 n n PA O1A GCP doub 149 n n PA O2A GCP sing 150 n n PA O5' GCP sing 151 n n O2A HOA2 GCP sing 152 n n O5' C5' GCP sing 153 n n C5' C4' GCP sing 154 n n C5' "H5'2" GCP sing 155 n n C5' "H5'1" GCP sing 156 n n C4' O4' GCP sing 157 n n C4' C3' GCP sing 158 n n C4' H4' GCP sing 159 n n O4' C1' GCP sing 160 n n C3' O3' GCP sing 161 n n C3' C2' GCP sing 162 n n C3' H3' GCP sing 163 n n O3' HO3' GCP sing 164 n n C2' O2' GCP sing 165 n n C2' C1' GCP sing 166 n n C2' H2' GCP sing 167 n n O2' HO2' GCP sing 168 n n C1' N9 GCP sing 169 n n C1' H1' GCP sing 170 n n N9 C8 GCP sing 171 n y N9 C4 GCP sing 172 n y C8 N7 GCP doub 173 n y C8 H8 GCP sing 174 n n N7 C5 GCP sing 175 n y C5 C6 GCP sing 176 n y C5 C4 GCP doub 177 n y C6 O6 GCP doub 178 n n C6 N1 GCP sing 179 n y N1 C2 GCP sing 180 n y N1 HN1 GCP sing 181 n n C2 N2 GCP sing 182 n n C2 N3 GCP doub 183 n y N2 HN21 GCP sing 184 n n N2 HN22 GCP sing 185 n n N3 C4 GCP sing 186 n y # _atom_sites.entry_id 4DST _atom_sites.fract_transf_matrix[1][1] 0.012671 _atom_sites.fract_transf_matrix[1][2] 0.007315 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014631 _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] 0.012718 _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 B 2 9LI A 1 201 1 9LI 9LI . C 3 GCP A 1 202 1 GCP GCP . D 4 MG A 1 203 1 MG MG . E 5 GOL A 1 204 5 GOL GOL . F 6 EDO A 1 205 6 EDO EDO . G 7 DMS A 1 206 7 DMS DMS . H 8 ACT A 1 207 8 ACT ACT . I 4 MG A 1 208 9 MG MG . J 9 HOH A 1 301 1 HOH HOH . J 9 HOH A 2 302 2 HOH HOH . J 9 HOH A 3 303 3 HOH HOH . J 9 HOH A 4 304 4 HOH HOH . J 9 HOH A 5 305 5 HOH HOH . J 9 HOH A 6 306 6 HOH HOH . J 9 HOH A 7 307 7 HOH HOH . J 9 HOH A 8 308 8 HOH HOH . J 9 HOH A 9 309 9 HOH HOH . J 9 HOH A 10 310 10 HOH HOH . J 9 HOH A 11 311 11 HOH HOH . J 9 HOH A 12 312 12 HOH HOH . J 9 HOH A 13 313 14 HOH HOH . J 9 HOH A 14 314 15 HOH HOH . J 9 HOH A 15 315 16 HOH HOH . J 9 HOH A 16 316 17 HOH HOH . J 9 HOH A 17 317 18 HOH HOH . J 9 HOH A 18 318 19 HOH HOH . J 9 HOH A 19 319 20 HOH HOH . J 9 HOH A 20 320 21 HOH HOH . J 9 HOH A 21 321 22 HOH HOH . J 9 HOH A 22 322 23 HOH HOH . J 9 HOH A 23 323 24 HOH HOH . J 9 HOH A 24 324 25 HOH HOH . J 9 HOH A 25 325 26 HOH HOH . J 9 HOH A 26 326 27 HOH HOH . J 9 HOH A 27 327 28 HOH HOH . J 9 HOH A 28 328 29 HOH HOH . J 9 HOH A 29 329 30 HOH HOH . J 9 HOH A 30 330 31 HOH HOH . J 9 HOH A 31 331 32 HOH HOH . J 9 HOH A 32 332 33 HOH HOH . J 9 HOH A 33 333 34 HOH HOH . J 9 HOH A 34 334 35 HOH HOH . J 9 HOH A 35 335 36 HOH HOH . J 9 HOH A 36 336 37 HOH HOH . J 9 HOH A 37 337 38 HOH HOH . J 9 HOH A 38 338 39 HOH HOH . J 9 HOH A 39 339 40 HOH HOH . J 9 HOH A 40 340 41 HOH HOH . J 9 HOH A 41 341 42 HOH HOH . J 9 HOH A 42 342 43 HOH HOH . J 9 HOH A 43 343 44 HOH HOH . J 9 HOH A 44 344 45 HOH HOH . J 9 HOH A 45 345 46 HOH HOH . J 9 HOH A 46 346 47 HOH HOH . J 9 HOH A 47 347 48 HOH HOH . J 9 HOH A 48 348 49 HOH HOH . J 9 HOH A 49 349 50 HOH HOH . J 9 HOH A 50 350 51 HOH HOH . J 9 HOH A 51 351 52 HOH HOH . J 9 HOH A 52 352 53 HOH HOH . J 9 HOH A 53 353 54 HOH HOH . J 9 HOH A 54 354 55 HOH HOH . J 9 HOH A 55 355 56 HOH HOH . J 9 HOH A 56 356 57 HOH HOH . J 9 HOH A 57 357 58 HOH HOH . J 9 HOH A 58 358 59 HOH HOH . J 9 HOH A 59 359 60 HOH HOH . J 9 HOH A 60 360 61 HOH HOH . J 9 HOH A 61 361 62 HOH HOH . J 9 HOH A 62 362 63 HOH HOH . J 9 HOH A 63 363 64 HOH HOH . J 9 HOH A 64 364 65 HOH HOH . J 9 HOH A 65 365 66 HOH HOH . J 9 HOH A 66 366 68 HOH HOH . J 9 HOH A 67 367 69 HOH HOH . J 9 HOH A 68 368 70 HOH HOH . J 9 HOH A 69 369 73 HOH HOH . J 9 HOH A 70 370 75 HOH HOH . J 9 HOH A 71 371 76 HOH HOH . J 9 HOH A 72 372 77 HOH HOH . J 9 HOH A 73 373 78 HOH HOH . J 9 HOH A 74 374 79 HOH HOH . J 9 HOH A 75 375 80 HOH HOH . J 9 HOH A 76 376 82 HOH HOH . J 9 HOH A 77 377 83 HOH HOH . J 9 HOH A 78 378 84 HOH HOH . J 9 HOH A 79 379 85 HOH HOH . J 9 HOH A 80 380 86 HOH HOH . J 9 HOH A 81 381 87 HOH HOH . J 9 HOH A 82 382 88 HOH HOH . J 9 HOH A 83 383 89 HOH HOH . J 9 HOH A 84 384 90 HOH HOH . J 9 HOH A 85 385 91 HOH HOH . J 9 HOH A 86 386 92 HOH HOH . J 9 HOH A 87 387 93 HOH HOH . J 9 HOH A 88 388 94 HOH HOH . J 9 HOH A 89 389 95 HOH HOH . J 9 HOH A 90 390 96 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 GCP . . . C 3 14.988 0.822 9.002 1 25.43 ? PG GCP 202 A 1 HETATM 2 O O1G GCP . . . C 3 16.239 1.557 9.373 1 27.28 ? O1G GCP 202 A 1 HETATM 3 O O2G GCP . . . C 3 14.391 0.084 10.167 1 27.49 ? O2G GCP 202 A 1 HETATM 4 O O3G GCP . . . C 3 14.009 1.694 8.258 1 30.09 ? O3G GCP 202 A 1 HETATM 5 C C3B GCP . . . C 3 15.455 -0.509 7.867 1 14.31 ? C3B GCP 202 A 1 HETATM 6 P PB GCP . . . C 3 16.345 0.048 6.384 1 23.42 ? PB GCP 202 A 1 HETATM 7 O O1B GCP . . . C 3 15.449 0.948 5.565 1 20.37 ? O1B GCP 202 A 1 HETATM 8 O O2B GCP . . . C 3 17.69 0.595 6.748 1 23.04 ? O2B GCP 202 A 1 HETATM 9 O O3A GCP . . . C 3 16.623 -1.273 5.512 1 23.25 ? O3A GCP 202 A 1 HETATM 10 P PA GCP . . . C 3 17.923 -2.21 5.673 1 24.57 ? PA GCP 202 A 1 HETATM 11 O O1A GCP . . . C 3 19.057 -1.658 4.848 1 26.52 ? O1A GCP 202 A 1 HETATM 12 O O2A GCP . . . C 3 18.135 -2.514 7.136 1 26.04 ? O2A GCP 202 A 1 HETATM 13 O O5' GCP . . . C 3 17.428 -3.541 4.923 1 24.06 ? O5' GCP 202 A 1 HETATM 14 C C5' GCP . . . C 3 16.166 -4.133 5.241 1 22.63 ? C5' GCP 202 A 1 HETATM 15 C C4' GCP . . . C 3 16.114 -5.543 4.668 1 23.09 ? C4' GCP 202 A 1 HETATM 16 O O4' GCP . . . C 3 16.076 -5.482 3.238 1 23.77 ? O4' GCP 202 A 1 HETATM 17 C C3' GCP . . . C 3 17.382 -6.294 5.027 1 24.66 ? C3' GCP 202 A 1 HETATM 18 O O3' GCP . . . C 3 17.037 -7.667 5.21 1 27.83 ? O3' GCP 202 A 1 HETATM 19 C C2' GCP . . . C 3 18.267 -6.14 3.807 1 27.41 ? C2' GCP 202 A 1 HETATM 20 O O2' GCP . . . C 3 19.145 -7.254 3.634 1 34.04 ? O2' GCP 202 A 1 HETATM 21 C C1' GCP . . . C 3 17.257 -6.069 2.679 1 24.92 ? C1' GCP 202 A 1 HETATM 22 N N9 GCP . . . C 3 17.754 -5.211 1.585 1 23.03 ? N9 GCP 202 A 1 HETATM 23 C C8 GCP . . . C 3 18.223 -3.958 1.704 1 16.12 ? C8 GCP 202 A 1 HETATM 24 N N7 GCP . . . C 3 18.579 -3.474 0.488 1 18.57 ? N7 GCP 202 A 1 HETATM 25 C C5 GCP . . . C 3 18.341 -4.432 -0.432 1 19.75 ? C5 GCP 202 A 1 HETATM 26 C C6 GCP . . . C 3 18.483 -4.59 -1.901 1 20.33 ? C6 GCP 202 A 1 HETATM 27 O O6 GCP . . . C 3 18.939 -3.672 -2.611 1 21.68 ? O6 GCP 202 A 1 HETATM 28 N N1 GCP . . . C 3 18.103 -5.749 -2.455 1 19.27 ? N1 GCP 202 A 1 HETATM 29 C C2 GCP . . . C 3 17.612 -6.764 -1.719 1 20.57 ? C2 GCP 202 A 1 HETATM 30 N N2 GCP . . . C 3 17.25 -7.912 -2.335 1 18.65 ? N2 GCP 202 A 1 HETATM 31 N N3 GCP . . . C 3 17.45 -6.687 -0.378 1 21.35 ? N3 GCP 202 A 1 HETATM 32 C C4 GCP . . . C 3 17.794 -5.573 0.302 1 20.56 ? C4 GCP 202 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #