data_6S5F # _model_server_result.job_id PPbgbI2xZzwvW8zeBQW94g _model_server_result.datetime_utc '2025-08-31 04:08:07' _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 6s5f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 6S5F # _exptl.entry_id 6S5F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC 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 107.51 _cell.angle_gamma 90 _cell.entry_id 6S5F _cell.length_a 52.725 _cell.length_b 35.285 _cell.length_c 53.605 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S5F _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 2 1' # _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 _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 OG SER 23 A SER 22 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc2 A OG1 THR 41 A THR 40 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc3 C O2G GNP . A GNP 302 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc4 C O1B GNP . A GNP 302 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc5 E MG MG . A MG 304 1_555 F O HOH . A HOH 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc6 E MG MG . A MG 304 1_555 F O HOH . A HOH 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC 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 GNP doub 138 n n PG O2G GNP sing 139 n n PG O3G GNP sing 140 n n PG N3B GNP sing 141 n n O2G HOG2 GNP sing 142 n n O3G HOG3 GNP sing 143 n n N3B PB GNP sing 144 n n N3B HNB3 GNP sing 145 n n PB O1B GNP doub 146 n n PB O2B GNP sing 147 n n PB O3A GNP sing 148 n n O2B HOB2 GNP sing 149 n n O3A PA GNP sing 150 n n PA O1A GNP doub 151 n n PA O2A GNP sing 152 n n PA O5' GNP sing 153 n n O2A HOA2 GNP sing 154 n n O5' C5' GNP sing 155 n n C5' C4' GNP sing 156 n n C5' "H5'2" GNP sing 157 n n C5' "H5'1" GNP sing 158 n n C4' O4' GNP sing 159 n n C4' C3' GNP sing 160 n n C4' H4' GNP sing 161 n n O4' C1' GNP sing 162 n n C3' O3' GNP sing 163 n n C3' C2' GNP sing 164 n n C3' H3' GNP sing 165 n n O3' HO3' GNP sing 166 n n C2' O2' GNP sing 167 n n C2' C1' GNP sing 168 n n C2' H2' GNP sing 169 n n O2' HO2' GNP sing 170 n n C1' N9 GNP sing 171 n n C1' H1' GNP sing 172 n n N9 C8 GNP sing 173 n y N9 C4 GNP sing 174 n y C8 N7 GNP doub 175 n y C8 H8 GNP sing 176 n n N7 C5 GNP sing 177 n y C5 C6 GNP sing 178 n y C5 C4 GNP doub 179 n y C6 O6 GNP doub 180 n n C6 N1 GNP sing 181 n y N1 C2 GNP sing 182 n y N1 HN1 GNP sing 183 n n C2 N2 GNP sing 184 n n C2 N3 GNP doub 185 n y N2 HN21 GNP sing 186 n n N2 HN22 GNP sing 187 n n N3 C4 GNP sing 188 n y # _atom_sites.entry_id 6S5F _atom_sites.fract_transf_matrix[1][1] 0.018966 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005985 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028341 _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] 0.019562 _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 GLY A 1 301 192 GLY GLY . C 3 GNP A 1 302 201 GNP GNP . D 4 EDO A 1 303 301 EDO EDO . E 5 MG A 1 304 1 MG MG . F 6 HOH A 1 401 39 HOH HOH . F 6 HOH A 2 402 66 HOH HOH . F 6 HOH A 3 403 112 HOH HOH . F 6 HOH A 4 404 110 HOH HOH . F 6 HOH A 5 405 114 HOH HOH . F 6 HOH A 6 406 116 HOH HOH . F 6 HOH A 7 407 30 HOH HOH . F 6 HOH A 8 408 65 HOH HOH . F 6 HOH A 9 409 14 HOH HOH . F 6 HOH A 10 410 79 HOH HOH . F 6 HOH A 11 411 34 HOH HOH . F 6 HOH A 12 412 29 HOH HOH . F 6 HOH A 13 413 40 HOH HOH . F 6 HOH A 14 414 54 HOH HOH . F 6 HOH A 15 415 74 HOH HOH . F 6 HOH A 16 416 4 HOH HOH . F 6 HOH A 17 417 111 HOH HOH . F 6 HOH A 18 418 50 HOH HOH . F 6 HOH A 19 419 78 HOH HOH . F 6 HOH A 20 420 37 HOH HOH . F 6 HOH A 21 421 59 HOH HOH . F 6 HOH A 22 422 105 HOH HOH . F 6 HOH A 23 423 95 HOH HOH . F 6 HOH A 24 424 100 HOH HOH . F 6 HOH A 25 425 88 HOH HOH . F 6 HOH A 26 426 91 HOH HOH . F 6 HOH A 27 427 26 HOH HOH . F 6 HOH A 28 428 18 HOH HOH . F 6 HOH A 29 429 64 HOH HOH . F 6 HOH A 30 430 1 HOH HOH . F 6 HOH A 31 431 3 HOH HOH . F 6 HOH A 32 432 6 HOH HOH . F 6 HOH A 33 433 13 HOH HOH . F 6 HOH A 34 434 83 HOH HOH . F 6 HOH A 35 435 9 HOH HOH . F 6 HOH A 36 436 25 HOH HOH . F 6 HOH A 37 437 20 HOH HOH . F 6 HOH A 38 438 15 HOH HOH . F 6 HOH A 39 439 38 HOH HOH . F 6 HOH A 40 440 69 HOH HOH . F 6 HOH A 41 441 85 HOH HOH . F 6 HOH A 42 442 7 HOH HOH . F 6 HOH A 43 443 24 HOH HOH . F 6 HOH A 44 444 21 HOH HOH . F 6 HOH A 45 445 62 HOH HOH . F 6 HOH A 46 446 102 HOH HOH . F 6 HOH A 47 447 36 HOH HOH . F 6 HOH A 48 448 89 HOH HOH . F 6 HOH A 49 449 70 HOH HOH . F 6 HOH A 50 450 103 HOH HOH . F 6 HOH A 51 451 93 HOH HOH . F 6 HOH A 52 452 32 HOH HOH . F 6 HOH A 53 453 43 HOH HOH . F 6 HOH A 54 454 27 HOH HOH . F 6 HOH A 55 455 60 HOH HOH . F 6 HOH A 56 456 12 HOH HOH . F 6 HOH A 57 457 118 HOH HOH . F 6 HOH A 58 458 23 HOH HOH . F 6 HOH A 59 459 77 HOH HOH . F 6 HOH A 60 460 61 HOH HOH . F 6 HOH A 61 461 48 HOH HOH . F 6 HOH A 62 462 5 HOH HOH . F 6 HOH A 63 463 63 HOH HOH . F 6 HOH A 64 464 58 HOH HOH . F 6 HOH A 65 465 97 HOH HOH . F 6 HOH A 66 466 56 HOH HOH . F 6 HOH A 67 467 115 HOH HOH . F 6 HOH A 68 468 46 HOH HOH . F 6 HOH A 69 469 10 HOH HOH . F 6 HOH A 70 470 22 HOH HOH . F 6 HOH A 71 471 109 HOH HOH . F 6 HOH A 72 472 19 HOH HOH . F 6 HOH A 73 473 55 HOH HOH . F 6 HOH A 74 474 52 HOH HOH . F 6 HOH A 75 475 101 HOH HOH . F 6 HOH A 76 476 28 HOH HOH . F 6 HOH A 77 477 49 HOH HOH . F 6 HOH A 78 478 2 HOH HOH . F 6 HOH A 79 479 16 HOH HOH . F 6 HOH A 80 480 33 HOH HOH . F 6 HOH A 81 481 35 HOH HOH . F 6 HOH A 82 482 31 HOH HOH . F 6 HOH A 83 483 17 HOH HOH . F 6 HOH A 84 484 73 HOH HOH . F 6 HOH A 85 485 71 HOH HOH . F 6 HOH A 86 486 81 HOH HOH . F 6 HOH A 87 487 67 HOH HOH . F 6 HOH A 88 488 80 HOH HOH . F 6 HOH A 89 489 47 HOH HOH . F 6 HOH A 90 490 53 HOH HOH . F 6 HOH A 91 491 90 HOH HOH . F 6 HOH A 92 492 117 HOH HOH . F 6 HOH A 93 493 76 HOH HOH . F 6 HOH A 94 494 42 HOH HOH . F 6 HOH A 95 495 107 HOH HOH . F 6 HOH A 96 496 120 HOH HOH . F 6 HOH A 97 497 87 HOH HOH . F 6 HOH A 98 498 41 HOH HOH . F 6 HOH A 99 499 45 HOH HOH . F 6 HOH A 100 500 72 HOH HOH . F 6 HOH A 101 501 44 HOH HOH . F 6 HOH A 102 502 119 HOH HOH . F 6 HOH A 103 503 96 HOH HOH . F 6 HOH A 104 504 121 HOH HOH . F 6 HOH A 105 505 51 HOH HOH . F 6 HOH A 106 506 122 HOH HOH . F 6 HOH A 107 507 94 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 GNP . . . C 3 23.157 -4.365 12.908 1 17.93 ? PG GNP 302 A 1 HETATM 2 O O1G GNP . . . C 3 24.6 -4.949 12.954 1 19.15 ? O1G GNP 302 A 1 HETATM 3 O O2G GNP . . . C 3 22.932 -3.511 14.17 1 18.09 ? O2G GNP 302 A 1 HETATM 4 O O3G GNP . . . C 3 22.18 -5.425 12.833 1 17.11 ? O3G GNP 302 A 1 HETATM 5 N N3B GNP . . . C 3 23.034 -3.354 11.589 1 17.49 ? N3B GNP 302 A 1 HETATM 6 P PB GNP . . . C 3 21.661 -2.479 11.178 1 18.4 ? PB GNP 302 A 1 HETATM 7 O O1B GNP . . . C 3 21.244 -1.728 12.416 1 14.86 ? O1B GNP 302 A 1 HETATM 8 O O2B GNP . . . C 3 20.599 -3.307 10.474 1 17.6 ? O2B GNP 302 A 1 HETATM 9 O O3A GNP . . . C 3 22.122 -1.332 10.239 1 17.26 ? O3A GNP 302 A 1 HETATM 10 P PA GNP . . . C 3 22.345 0.246 10.4 1 18.61 ? PA GNP 302 A 1 HETATM 11 O O1A GNP . . . C 3 23.445 0.428 11.356 1 19.48 ? O1A GNP 302 A 1 HETATM 12 O O2A GNP . . . C 3 20.995 0.825 10.637 1 16.36 ? O2A GNP 302 A 1 HETATM 13 O O5' GNP . . . C 3 22.773 0.68 8.933 1 18.01 ? O5' GNP 302 A 1 HETATM 14 C C5' GNP . . . C 3 23.941 0.057 8.351 1 20.22 ? C5' GNP 302 A 1 HETATM 15 C C4' GNP . . . C 3 24.446 0.908 7.212 1 21.82 ? C4' GNP 302 A 1 HETATM 16 O O4' GNP . . . C 3 23.381 1.185 6.265 1 20.98 ? O4' GNP 302 A 1 HETATM 17 C C3' GNP . . . C 3 24.995 2.284 7.615 1 25.5 ? C3' GNP 302 A 1 HETATM 18 O O3' GNP . . . C 3 26.07 2.629 6.756 1 28.54 ? O3' GNP 302 A 1 HETATM 19 C C2' GNP . . . C 3 23.797 3.202 7.379 1 21.34 ? C2' GNP 302 A 1 HETATM 20 O O2' GNP . . . C 3 24.072 4.552 7.073 1 22.08 ? O2' GNP 302 A 1 HETATM 21 C C1' GNP . . . C 3 23.215 2.581 6.125 1 18.89 ? C1' GNP 302 A 1 HETATM 22 N N9 GNP . . . C 3 21.801 2.887 5.917 1 18.61 ? N9 GNP 302 A 1 HETATM 23 C C8 GNP . . . C 3 20.786 2.617 6.8 1 17.86 ? C8 GNP 302 A 1 HETATM 24 N N7 GNP . . . C 3 19.605 2.957 6.35 1 16.66 ? N7 GNP 302 A 1 HETATM 25 C C5 GNP . . . C 3 19.853 3.427 5.061 1 17.04 ? C5 GNP 302 A 1 HETATM 26 C C6 GNP . . . C 3 18.965 3.943 4.065 1 19.17 ? C6 GNP 302 A 1 HETATM 27 O O6 GNP . . . C 3 17.727 4.088 4.077 1 18.77 ? O6 GNP 302 A 1 HETATM 28 N N1 GNP . . . C 3 19.652 4.268 2.889 1 17.92 ? N1 GNP 302 A 1 HETATM 29 C C2 GNP . . . C 3 21.019 4.246 2.717 1 19.08 ? C2 GNP 302 A 1 HETATM 30 N N2 GNP . . . C 3 21.483 4.673 1.514 1 19.89 ? N2 GNP 302 A 1 HETATM 31 N N3 GNP . . . C 3 21.854 3.781 3.638 1 18.83 ? N3 GNP 302 A 1 HETATM 32 C C4 GNP . . . C 3 21.209 3.399 4.791 1 17.43 ? C4 GNP 302 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 661 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #