data_3C5H # _model_server_result.job_id tpEHEPVSBc28EGV0QPcsDQ _model_server_result.datetime_utc '2024-11-10 02:07:33' _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 3c5h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 3C5H # _exptl.entry_id 3C5H _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 90 _cell.angle_gamma 90 _cell.entry_id 3C5H _cell.length_a 108.959 _cell.length_b 108.959 _cell.length_c 51.319 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C5H _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details 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 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 42 A SER 36 1_555 B MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc2 A OE2 GLU 101 A GLU 95 1_555 B MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc3 D O2G GNP . A GNP 301 1_555 B MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc4 D O2B GNP . A GNP 301 1_555 B MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc5 B MG MG . A MG 302 1_555 J O HOH . A HOH 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc6 B MG MG . A MG 302 1_555 J O HOH . A HOH 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc7 C MG MG . A MG 303 1_555 J O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc8 C MG MG . A MG 303 1_555 J O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc9 C MG MG . A MG 303 1_555 J O HOH . A HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc10 C MG MG . A MG 303 1_555 J O HOH . A HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc11 C MG MG . A MG 303 1_555 J O HOH . A HOH 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc12 C MG MG . A MG 303 1_555 J O HOH . A HOH 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? # _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 3C5H _atom_sites.fract_transf_matrix[1][1] 0.009178 _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] 0.009178 _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] 0.019486 _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 MG A 1 302 302 MG MG . C 2 MG A 1 303 303 MG MG . D 3 GNP A 1 301 301 GNP GNP . E 4 UNX A 1 304 304 UNX UNX . F 4 UNX A 1 305 305 UNX UNX . G 4 UNX A 1 306 306 UNX UNX . H 4 UNX A 1 307 307 UNX UNX . I 4 UNX A 1 308 308 UNX UNX . J 5 HOH A 1 309 1 HOH HOH . J 5 HOH A 2 310 2 HOH HOH . J 5 HOH A 3 311 3 HOH HOH . J 5 HOH A 4 312 4 HOH HOH . J 5 HOH A 5 313 5 HOH HOH . J 5 HOH A 6 314 6 HOH HOH . J 5 HOH A 7 315 7 HOH HOH . J 5 HOH A 8 316 8 HOH HOH . J 5 HOH A 9 317 9 HOH HOH . J 5 HOH A 10 318 10 HOH HOH . J 5 HOH A 11 319 11 HOH HOH . J 5 HOH A 12 320 12 HOH HOH . J 5 HOH A 13 321 13 HOH HOH . J 5 HOH A 14 322 14 HOH HOH . J 5 HOH A 15 323 15 HOH HOH . J 5 HOH A 16 324 16 HOH HOH . J 5 HOH A 17 325 17 HOH HOH . J 5 HOH A 18 326 18 HOH HOH . J 5 HOH A 19 327 19 HOH HOH . J 5 HOH A 20 328 20 HOH HOH . J 5 HOH A 21 329 21 HOH HOH . J 5 HOH A 22 330 22 HOH HOH . J 5 HOH A 23 331 23 HOH HOH . J 5 HOH A 24 332 24 HOH HOH . J 5 HOH A 25 333 25 HOH HOH . J 5 HOH A 26 334 26 HOH HOH . J 5 HOH A 27 335 27 HOH HOH . J 5 HOH A 28 336 28 HOH HOH . J 5 HOH A 29 337 29 HOH HOH . J 5 HOH A 30 338 30 HOH HOH . J 5 HOH A 31 339 31 HOH HOH . J 5 HOH A 32 340 32 HOH HOH . J 5 HOH A 33 341 33 HOH HOH . J 5 HOH A 34 342 34 HOH HOH . J 5 HOH A 35 343 35 HOH HOH . J 5 HOH A 36 344 36 HOH HOH . J 5 HOH A 37 345 37 HOH HOH . J 5 HOH A 38 346 38 HOH HOH . J 5 HOH A 39 347 39 HOH HOH . J 5 HOH A 40 348 40 HOH HOH . J 5 HOH A 41 349 41 HOH HOH . J 5 HOH A 42 350 42 HOH HOH . J 5 HOH A 43 351 43 HOH HOH . J 5 HOH A 44 352 44 HOH HOH . J 5 HOH A 45 353 45 HOH HOH . J 5 HOH A 46 354 46 HOH HOH . J 5 HOH A 47 355 47 HOH HOH . J 5 HOH A 48 356 48 HOH HOH . J 5 HOH A 49 357 49 HOH HOH . J 5 HOH A 50 358 50 HOH HOH . J 5 HOH A 51 359 51 HOH HOH . J 5 HOH A 52 360 52 HOH HOH . J 5 HOH A 53 361 53 HOH HOH . J 5 HOH A 54 362 54 HOH HOH . J 5 HOH A 55 363 55 HOH HOH . J 5 HOH A 56 364 56 HOH HOH . J 5 HOH A 57 365 57 HOH HOH . J 5 HOH A 58 366 58 HOH HOH . J 5 HOH A 59 367 59 HOH HOH . J 5 HOH A 60 368 60 HOH HOH . J 5 HOH A 61 369 61 HOH HOH . J 5 HOH A 62 370 62 HOH HOH . J 5 HOH A 63 371 63 HOH HOH . J 5 HOH A 64 372 64 HOH HOH . J 5 HOH A 65 373 65 HOH HOH . J 5 HOH A 66 374 66 HOH HOH . J 5 HOH A 67 375 67 HOH HOH . J 5 HOH A 68 376 68 HOH HOH . J 5 HOH A 69 377 69 HOH HOH . J 5 HOH A 70 378 70 HOH HOH . J 5 HOH A 71 379 71 HOH HOH . J 5 HOH A 72 380 72 HOH HOH . J 5 HOH A 73 381 73 HOH HOH . J 5 HOH A 74 382 74 HOH HOH . J 5 HOH A 75 383 75 HOH HOH . J 5 HOH A 76 384 76 HOH HOH . J 5 HOH A 77 385 77 HOH HOH . J 5 HOH A 78 386 78 HOH HOH . J 5 HOH A 79 387 79 HOH HOH . J 5 HOH A 80 388 80 HOH HOH . J 5 HOH A 81 389 81 HOH HOH . J 5 HOH A 82 390 82 HOH HOH . J 5 HOH A 83 391 83 HOH HOH . J 5 HOH A 84 392 84 HOH HOH . J 5 HOH A 85 393 85 HOH HOH . J 5 HOH A 86 394 86 HOH HOH . J 5 HOH A 87 395 87 HOH HOH . J 5 HOH A 88 396 88 HOH HOH . J 5 HOH A 89 397 89 HOH HOH . J 5 HOH A 90 398 90 HOH HOH . J 5 HOH A 91 399 91 HOH HOH . J 5 HOH A 92 400 92 HOH HOH . J 5 HOH A 93 401 93 HOH HOH . J 5 HOH A 94 402 94 HOH HOH . J 5 HOH A 95 403 95 HOH HOH . J 5 HOH A 96 404 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 GNP . . . D 3 12.116 46.116 11.892 1 16.89 ? PG GNP 301 A 1 HETATM 2 O O1G GNP . . . D 3 11.022 45.453 11.107 1 13.7 ? O1G GNP 301 A 1 HETATM 3 O O2G GNP . . . D 3 13.413 46.512 11.226 1 19.64 ? O2G GNP 301 A 1 HETATM 4 O O3G GNP . . . D 3 11.493 47.267 12.728 1 19.93 ? O3G GNP 301 A 1 HETATM 5 N N3B GNP . . . D 3 12.457 45.049 13.045 1 12.78 ? N3B GNP 301 A 1 HETATM 6 P PB GNP . . . D 3 13.596 43.884 12.949 1 15.75 ? PB GNP 301 A 1 HETATM 7 O O1B GNP . . . D 3 13.095 42.761 12.207 1 16.37 ? O1B GNP 301 A 1 HETATM 8 O O2B GNP . . . D 3 14.823 44.566 12.561 1 15.47 ? O2B GNP 301 A 1 HETATM 9 O O3A GNP . . . D 3 13.731 43.393 14.457 1 15.44 ? O3A GNP 301 A 1 HETATM 10 P PA GNP . . . D 3 14.833 43.728 15.531 1 18.32 ? PA GNP 301 A 1 HETATM 11 O O1A GNP . . . D 3 16.11 43.031 15.172 1 15.63 ? O1A GNP 301 A 1 HETATM 12 O O2A GNP . . . D 3 15.013 45.17 15.774 1 18.13 ? O2A GNP 301 A 1 HETATM 13 O O5' GNP . . . D 3 14.285 43.019 16.807 1 20.07 ? O5' GNP 301 A 1 HETATM 14 C C5' GNP . . . D 3 13.057 43.465 17.414 1 22.81 ? C5' GNP 301 A 1 HETATM 15 C C4' GNP . . . D 3 13.174 43.136 18.887 1 26.4 ? C4' GNP 301 A 1 HETATM 16 O O4' GNP . . . D 3 13.127 41.687 19.023 1 22.96 ? O4' GNP 301 A 1 HETATM 17 C C3' GNP . . . D 3 14.507 43.543 19.504 1 27.17 ? C3' GNP 301 A 1 HETATM 18 O O3' GNP . . . D 3 14.502 44.897 19.991 1 32.48 ? O3' GNP 301 A 1 HETATM 19 C C2' GNP . . . D 3 14.66 42.581 20.649 1 30.11 ? C2' GNP 301 A 1 HETATM 20 O O2' GNP . . . D 3 13.866 43.011 21.756 1 34.49 ? O2' GNP 301 A 1 HETATM 21 C C1' GNP . . . D 3 14.08 41.315 20.033 1 23.05 ? C1' GNP 301 A 1 HETATM 22 N N9 GNP . . . D 3 15.077 40.351 19.526 1 22.68 ? N9 GNP 301 A 1 HETATM 23 C C8 GNP . . . D 3 15.894 40.407 18.403 1 23.16 ? C8 GNP 301 A 1 HETATM 24 N N7 GNP . . . D 3 16.649 39.328 18.26 1 20.38 ? N7 GNP 301 A 1 HETATM 25 C C5 GNP . . . D 3 16.313 38.533 19.349 1 20.69 ? C5 GNP 301 A 1 HETATM 26 C C6 GNP . . . D 3 16.774 37.246 19.745 1 23.44 ? C6 GNP 301 A 1 HETATM 27 O O6 GNP . . . D 3 17.625 36.521 19.182 1 20.59 ? O6 GNP 301 A 1 HETATM 28 N N1 GNP . . . D 3 16.136 36.779 20.904 1 22.04 ? N1 GNP 301 A 1 HETATM 29 C C2 GNP . . . D 3 15.186 37.477 21.632 1 25.63 ? C2 GNP 301 A 1 HETATM 30 N N2 GNP . . . D 3 14.671 36.904 22.742 1 22.91 ? N2 GNP 301 A 1 HETATM 31 N N3 GNP . . . D 3 14.763 38.68 21.258 1 24.38 ? N3 GNP 301 A 1 HETATM 32 C C4 GNP . . . D 3 15.364 39.16 20.133 1 23.3 ? C4 GNP 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #