data_4L9W # _model_server_result.job_id '_dTQSbwT8F4aOcnRhHKd-A' _model_server_result.datetime_utc '2024-11-26 01:14:36' _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 4l9w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4L9W # _exptl.entry_id 4L9W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _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 90 _cell.angle_gamma 120 _cell.entry_id 4L9W _cell.length_a 89.148 _cell.length_b 89.148 _cell.length_c 136.314 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L9W _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # 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 software_defined_assembly 1 PISA dimeric 2 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,C,D,E,F 1 1,2 A,B,C,D,E,F 2 1,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 17_555 x-y+1/3,-y+2/3,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 51.469622 90.876 3 'crystal symmetry operation' 10_455 y-1/3,x+1/3,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 -44.574 25.734811 45.438 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 22 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A O PHE 33 A PHE 28 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc3 A OD1 ASP 35 A ASP 30 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc4 A OG1 THR 40 A THR 35 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc5 A OD1 ASP 159 A ASP 154 1_555 E CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc6 A OD2 ASP 159 A ASP 154 1_555 E CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.2 ? metalc ? metalc7 B O2B GNP . A GNP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc8 B O1G GNP . A GNP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc9 C MG MG . A MG 202 1_555 F O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc10 C MG MG . A MG 202 1_555 F O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc11 D CA CA . A CA 203 1_555 F O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc12 D CA CA . A CA 203 1_555 F O HOH . A HOH 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc13 E CA CA . A CA 204 1_555 F O HOH . A HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? # _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 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 4L9W _atom_sites.fract_transf_matrix[1][1] 0.011217 _atom_sites.fract_transf_matrix[1][2] 0.006476 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012953 _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] 0.007336 _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 GNP A 1 201 220 GNP GNP . C 3 MG A 1 202 200 MG MG . D 4 CA A 1 203 205 CA CA . E 4 CA A 1 204 207 CA CA . F 5 HOH A 1 301 1 HOH HOH . F 5 HOH A 2 302 2 HOH HOH . F 5 HOH A 3 303 3 HOH HOH . F 5 HOH A 4 304 4 HOH HOH . F 5 HOH A 5 305 5 HOH HOH . F 5 HOH A 6 306 6 HOH HOH . F 5 HOH A 7 307 7 HOH HOH . F 5 HOH A 8 308 8 HOH HOH . F 5 HOH A 9 309 9 HOH HOH . F 5 HOH A 10 310 10 HOH HOH . F 5 HOH A 11 311 11 HOH HOH . F 5 HOH A 12 312 12 HOH HOH . F 5 HOH A 13 313 13 HOH HOH . F 5 HOH A 14 314 14 HOH HOH . F 5 HOH A 15 315 15 HOH HOH . F 5 HOH A 16 316 16 HOH HOH . F 5 HOH A 17 317 17 HOH HOH . F 5 HOH A 18 318 18 HOH HOH . F 5 HOH A 19 319 19 HOH HOH . F 5 HOH A 20 320 20 HOH HOH . F 5 HOH A 21 321 21 HOH HOH . F 5 HOH A 22 322 22 HOH HOH . F 5 HOH A 23 323 23 HOH HOH . F 5 HOH A 24 324 24 HOH HOH . F 5 HOH A 25 325 25 HOH HOH . F 5 HOH A 26 326 26 HOH HOH . F 5 HOH A 27 327 27 HOH HOH . F 5 HOH A 28 328 28 HOH HOH . F 5 HOH A 29 329 29 HOH HOH . F 5 HOH A 30 330 30 HOH HOH . F 5 HOH A 31 331 31 HOH HOH . F 5 HOH A 32 332 32 HOH HOH . F 5 HOH A 33 333 33 HOH HOH . F 5 HOH A 34 334 34 HOH HOH . F 5 HOH A 35 335 35 HOH HOH . F 5 HOH A 36 336 36 HOH HOH . F 5 HOH A 37 337 37 HOH HOH . F 5 HOH A 38 338 38 HOH HOH . F 5 HOH A 39 339 39 HOH HOH . F 5 HOH A 40 340 40 HOH HOH . F 5 HOH A 41 341 41 HOH HOH . F 5 HOH A 42 342 42 HOH HOH . F 5 HOH A 43 343 43 HOH HOH . F 5 HOH A 44 344 44 HOH HOH . F 5 HOH A 45 345 45 HOH HOH . F 5 HOH A 46 346 46 HOH HOH . F 5 HOH A 47 347 47 HOH HOH . F 5 HOH A 48 348 48 HOH HOH . F 5 HOH A 49 349 49 HOH HOH . F 5 HOH A 50 350 50 HOH HOH . F 5 HOH A 51 351 51 HOH HOH . F 5 HOH A 52 352 52 HOH HOH . F 5 HOH A 53 353 53 HOH HOH . F 5 HOH A 54 354 54 HOH HOH . F 5 HOH A 55 355 55 HOH HOH . F 5 HOH A 56 356 56 HOH HOH . F 5 HOH A 57 357 57 HOH HOH . F 5 HOH A 58 358 58 HOH HOH . F 5 HOH A 59 359 59 HOH HOH . F 5 HOH A 60 360 60 HOH HOH . F 5 HOH A 61 361 61 HOH HOH . F 5 HOH A 62 362 62 HOH HOH . F 5 HOH A 63 363 63 HOH HOH . F 5 HOH A 64 364 64 HOH HOH . F 5 HOH A 65 365 65 HOH HOH . F 5 HOH A 66 366 66 HOH HOH . F 5 HOH A 67 367 67 HOH HOH . F 5 HOH A 68 368 68 HOH HOH . F 5 HOH A 69 369 69 HOH HOH . F 5 HOH A 70 370 70 HOH HOH . F 5 HOH A 71 371 71 HOH HOH . F 5 HOH A 72 372 72 HOH HOH . F 5 HOH A 73 373 73 HOH HOH . F 5 HOH A 74 374 74 HOH HOH . F 5 HOH A 75 375 75 HOH HOH . F 5 HOH A 76 376 76 HOH HOH . F 5 HOH A 77 377 77 HOH HOH . F 5 HOH A 78 378 78 HOH HOH . F 5 HOH A 79 379 79 HOH HOH . F 5 HOH A 80 380 80 HOH HOH . F 5 HOH A 81 381 81 HOH HOH . F 5 HOH A 82 382 82 HOH HOH . F 5 HOH A 83 383 83 HOH HOH . F 5 HOH A 84 384 84 HOH HOH . F 5 HOH A 85 385 85 HOH HOH . F 5 HOH A 86 386 86 HOH HOH . F 5 HOH A 87 387 87 HOH HOH . F 5 HOH A 88 388 88 HOH HOH . F 5 HOH A 89 389 89 HOH HOH . F 5 HOH A 90 390 90 HOH HOH . F 5 HOH A 91 391 91 HOH HOH . F 5 HOH A 92 392 92 HOH HOH . F 5 HOH A 93 393 93 HOH HOH . F 5 HOH A 94 394 94 HOH HOH . F 5 HOH A 95 395 95 HOH HOH . F 5 HOH A 96 396 96 HOH HOH . F 5 HOH A 97 397 97 HOH HOH . F 5 HOH A 98 398 98 HOH HOH . F 5 HOH A 99 399 99 HOH HOH . F 5 HOH A 100 400 100 HOH HOH . F 5 HOH A 101 401 101 HOH HOH . F 5 HOH A 102 402 102 HOH HOH . F 5 HOH A 103 403 103 HOH HOH . F 5 HOH A 104 404 104 HOH HOH . F 5 HOH A 105 405 105 HOH HOH . F 5 HOH A 106 406 106 HOH HOH . F 5 HOH A 107 407 107 HOH HOH . F 5 HOH A 108 408 108 HOH HOH . F 5 HOH A 109 409 109 HOH HOH . F 5 HOH A 110 410 110 HOH HOH . F 5 HOH A 111 411 111 HOH HOH . F 5 HOH A 112 412 112 HOH HOH . F 5 HOH A 113 413 113 HOH HOH . F 5 HOH A 114 414 114 HOH HOH . F 5 HOH A 115 415 115 HOH HOH . F 5 HOH A 116 416 116 HOH HOH . F 5 HOH A 117 417 117 HOH HOH . F 5 HOH A 118 418 118 HOH HOH . F 5 HOH A 119 419 119 HOH HOH . F 5 HOH A 120 420 120 HOH HOH . F 5 HOH A 121 421 121 HOH HOH . F 5 HOH A 122 422 122 HOH HOH . F 5 HOH A 123 423 123 HOH HOH . F 5 HOH A 124 424 124 HOH HOH . F 5 HOH A 125 425 125 HOH HOH . F 5 HOH A 126 426 126 HOH HOH . F 5 HOH A 127 427 127 HOH HOH . F 5 HOH A 128 428 128 HOH HOH . F 5 HOH A 129 429 129 HOH HOH . F 5 HOH A 130 430 130 HOH HOH . F 5 HOH A 131 431 131 HOH HOH . F 5 HOH A 132 432 132 HOH HOH . F 5 HOH A 133 433 133 HOH HOH . F 5 HOH A 134 434 134 HOH HOH . F 5 HOH A 135 435 135 HOH HOH . F 5 HOH A 136 436 136 HOH HOH . F 5 HOH A 137 437 137 HOH HOH . F 5 HOH A 138 438 138 HOH HOH . F 5 HOH A 139 439 139 HOH HOH . F 5 HOH A 140 440 140 HOH HOH . F 5 HOH A 141 441 141 HOH HOH . F 5 HOH A 142 442 142 HOH HOH . F 5 HOH A 143 443 143 HOH HOH . F 5 HOH A 144 444 144 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 . . . B 2 -6.834 15.155 22.854 1 25.62 ? PG GNP 201 A 1 HETATM 2 O O1G GNP . . . B 2 -7.118 16.562 22.436 1 24.76 ? O1G GNP 201 A 1 HETATM 3 O O2G GNP . . . B 2 -7.07 14.168 21.71 1 21.19 ? O2G GNP 201 A 1 HETATM 4 O O3G GNP . . . B 2 -5.424 15.227 23.363 1 30.08 ? O3G GNP 201 A 1 HETATM 5 N N3B GNP . . . B 2 -7.793 14.665 24.079 1 28.31 ? N3B GNP 201 A 1 HETATM 6 P PB GNP . . . B 2 -8.156 15.439 25.459 1 22.54 ? PB GNP 201 A 1 HETATM 7 O O1B GNP . . . B 2 -7.071 15.306 26.463 1 22.17 ? O1B GNP 201 A 1 HETATM 8 O O2B GNP . . . B 2 -8.483 16.845 25.128 1 21.06 ? O2B GNP 201 A 1 HETATM 9 O O3A GNP . . . B 2 -9.388 14.731 26.085 1 23.75 ? O3A GNP 201 A 1 HETATM 10 P PA GNP . . . B 2 -10.871 15.207 26.065 1 23.73 ? PA GNP 201 A 1 HETATM 11 O O1A GNP . . . B 2 -10.982 16.417 26.932 1 22.62 ? O1A GNP 201 A 1 HETATM 12 O O2A GNP . . . B 2 -11.398 15.362 24.677 1 26.24 ? O2A GNP 201 A 1 HETATM 13 O O5' GNP . . . B 2 -11.624 14.035 26.784 1 21.29 ? O5' GNP 201 A 1 HETATM 14 C C5' GNP . . . B 2 -11.584 12.695 26.241 1 22.93 ? C5' GNP 201 A 1 HETATM 15 C C4' GNP . . . B 2 -12.764 11.911 26.781 1 21.68 ? C4' GNP 201 A 1 HETATM 16 O O4' GNP . . . B 2 -12.654 11.799 28.223 1 25.16 ? O4' GNP 201 A 1 HETATM 17 C C3' GNP . . . B 2 -14.113 12.579 26.526 1 23.43 ? C3' GNP 201 A 1 HETATM 18 O O3' GNP . . . B 2 -15.071 11.577 26.285 1 25.39 ? O3' GNP 201 A 1 HETATM 19 C C2' GNP . . . B 2 -14.417 13.308 27.844 1 24.27 ? C2' GNP 201 A 1 HETATM 20 O O2' GNP . . . B 2 -15.804 13.448 28.078 1 21.77 ? O2' GNP 201 A 1 HETATM 21 C C1' GNP . . . B 2 -13.804 12.351 28.859 1 23.46 ? C1' GNP 201 A 1 HETATM 22 N N9 GNP . . . B 2 -13.389 13.021 30.089 1 21.71 ? N9 GNP 201 A 1 HETATM 23 C C8 GNP . . . B 2 -12.548 14.105 30.191 1 22.52 ? C8 GNP 201 A 1 HETATM 24 N N7 GNP . . . B 2 -12.363 14.494 31.418 1 20.97 ? N7 GNP 201 A 1 HETATM 25 C C5 GNP . . . B 2 -13.113 13.603 32.181 1 19.87 ? C5 GNP 201 A 1 HETATM 26 C C6 GNP . . . B 2 -13.303 13.532 33.58 1 22.84 ? C6 GNP 201 A 1 HETATM 27 O O6 GNP . . . B 2 -12.816 14.265 34.46 1 25.14 ? O6 GNP 201 A 1 HETATM 28 N N1 GNP . . . B 2 -14.157 12.486 33.943 1 20.76 ? N1 GNP 201 A 1 HETATM 29 C C2 GNP . . . B 2 -14.747 11.613 33.049 1 25.92 ? C2 GNP 201 A 1 HETATM 30 N N2 GNP . . . B 2 -15.545 10.664 33.561 1 23.55 ? N2 GNP 201 A 1 HETATM 31 N N3 GNP . . . B 2 -14.58 11.675 31.735 1 21.42 ? N3 GNP 201 A 1 HETATM 32 C C4 GNP . . . B 2 -13.754 12.694 31.372 1 21.26 ? C4 GNP 201 A 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #