data_8P3J # _model_server_result.job_id EXK-zec--ENPTtTlstabPA _model_server_result.datetime_utc '2024-11-22 08:15:37' _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 8p3j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":202}' # _entry.id 8P3J # _exptl.entry_id 8P3J _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 2 _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 8P3J _cell.length_a 62.436 _cell.length_b 75.828 _cell.length_c 118.53 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8P3J _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _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,I,J,K,L,M,N,O _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 I N 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 OG1 THR 61 A THR 23 1_555 G MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc2 A OG1 THR 79 A THR 41 1_555 G MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc3 E O1G GNP . A GNP 203 1_555 G MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc4 E O2B GNP . A GNP 203 1_555 G MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc5 G MG MG . A MG 205 1_555 N O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc6 G MG MG . A MG 205 1_555 N O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc7 B OG1 THR 61 B THR 23 1_555 M MG MG . B MG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc8 B OG1 THR 79 B THR 41 1_555 M MG MG . B MG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc9 I O1G GNP . B GNP 202 1_555 M MG MG . B MG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc10 I O1B GNP . B GNP 202 1_555 M MG MG . B MG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc11 M MG MG . B MG 206 1_555 O O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc12 M MG MG . B MG 206 1_555 O O HOH . B HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? # _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 8P3J _atom_sites.fract_transf_matrix[1][1] 0.016016 _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] 0.013188 _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] 0.008437 _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 2 WT6 A 1 201 201 WT6 C01 . D 2 WT6 A 1 202 301 WT6 C01 . E 3 GNP A 1 203 401 GNP GNP . F 4 GOL A 1 204 501 GOL GOL . G 5 MG A 1 205 4 MG MG . H 2 WT6 B 1 201 201 WT6 C01 . I 3 GNP B 1 202 301 GNP GNP . J 2 WT6 B 1 203 401 WT6 C01 . K 4 GOL B 1 204 501 GOL GOL . L 4 GOL B 1 205 601 GOL GOL . M 5 MG B 1 206 3 MG MG . N 6 HOH A 1 301 16 HOH HOH . N 6 HOH A 2 302 79 HOH HOH . N 6 HOH A 3 303 9 HOH HOH . N 6 HOH A 4 304 29 HOH HOH . N 6 HOH A 5 305 64 HOH HOH . N 6 HOH A 6 306 55 HOH HOH . N 6 HOH A 7 307 8 HOH HOH . N 6 HOH A 8 308 59 HOH HOH . N 6 HOH A 9 309 67 HOH HOH . N 6 HOH A 10 310 75 HOH HOH . N 6 HOH A 11 311 21 HOH HOH . N 6 HOH A 12 312 96 HOH HOH . N 6 HOH A 13 313 56 HOH HOH . N 6 HOH A 14 314 31 HOH HOH . N 6 HOH A 15 315 88 HOH HOH . N 6 HOH A 16 316 30 HOH HOH . N 6 HOH A 17 317 77 HOH HOH . N 6 HOH A 18 318 17 HOH HOH . N 6 HOH A 19 319 86 HOH HOH . N 6 HOH A 20 320 62 HOH HOH . N 6 HOH A 21 321 50 HOH HOH . N 6 HOH A 22 322 4 HOH HOH . N 6 HOH A 23 323 53 HOH HOH . N 6 HOH A 24 324 23 HOH HOH . N 6 HOH A 25 325 92 HOH HOH . N 6 HOH A 26 326 12 HOH HOH . N 6 HOH A 27 327 93 HOH HOH . N 6 HOH A 28 328 60 HOH HOH . N 6 HOH A 29 329 66 HOH HOH . N 6 HOH A 30 330 15 HOH HOH . N 6 HOH A 31 331 58 HOH HOH . N 6 HOH A 32 332 83 HOH HOH . N 6 HOH A 33 333 70 HOH HOH . N 6 HOH A 34 334 80 HOH HOH . N 6 HOH A 35 335 34 HOH HOH . N 6 HOH A 36 336 65 HOH HOH . N 6 HOH A 37 337 63 HOH HOH . N 6 HOH A 38 338 72 HOH HOH . N 6 HOH A 39 339 76 HOH HOH . N 6 HOH A 40 340 87 HOH HOH . N 6 HOH A 41 341 89 HOH HOH . N 6 HOH A 42 342 52 HOH HOH . N 6 HOH A 43 343 101 HOH HOH . N 6 HOH A 44 344 27 HOH HOH . N 6 HOH A 45 345 103 HOH HOH . N 6 HOH A 46 346 97 HOH HOH . N 6 HOH A 47 347 73 HOH HOH . N 6 HOH A 48 348 102 HOH HOH . N 6 HOH A 49 349 74 HOH HOH . N 6 HOH A 50 350 26 HOH HOH . N 6 HOH A 51 351 71 HOH HOH . N 6 HOH A 52 352 54 HOH HOH . N 6 HOH A 53 353 90 HOH HOH . N 6 HOH A 54 354 94 HOH HOH . N 6 HOH A 55 355 98 HOH HOH . N 6 HOH A 56 356 57 HOH HOH . N 6 HOH A 57 357 48 HOH HOH . N 6 HOH A 58 358 61 HOH HOH . N 6 HOH A 59 359 81 HOH HOH . N 6 HOH A 60 360 49 HOH HOH . N 6 HOH A 61 361 78 HOH HOH . N 6 HOH A 62 362 82 HOH HOH . N 6 HOH A 63 363 51 HOH HOH . N 6 HOH A 64 364 47 HOH HOH . N 6 HOH A 65 365 69 HOH HOH . N 6 HOH A 66 366 68 HOH HOH . N 6 HOH A 67 367 84 HOH HOH . N 6 HOH A 68 368 85 HOH HOH . O 6 HOH B 1 301 22 HOH HOH . O 6 HOH B 2 302 25 HOH HOH . O 6 HOH B 3 303 6 HOH HOH . O 6 HOH B 4 304 20 HOH HOH . O 6 HOH B 5 305 38 HOH HOH . O 6 HOH B 6 306 13 HOH HOH . O 6 HOH B 7 307 18 HOH HOH . O 6 HOH B 8 308 41 HOH HOH . O 6 HOH B 9 309 42 HOH HOH . O 6 HOH B 10 310 10 HOH HOH . O 6 HOH B 11 311 5 HOH HOH . O 6 HOH B 12 312 7 HOH HOH . O 6 HOH B 13 313 1 HOH HOH . O 6 HOH B 14 314 99 HOH HOH . O 6 HOH B 15 315 35 HOH HOH . O 6 HOH B 16 316 45 HOH HOH . O 6 HOH B 17 317 2 HOH HOH . O 6 HOH B 18 318 100 HOH HOH . O 6 HOH B 19 319 46 HOH HOH . O 6 HOH B 20 320 36 HOH HOH . O 6 HOH B 21 321 91 HOH HOH . O 6 HOH B 22 322 43 HOH HOH . O 6 HOH B 23 323 24 HOH HOH . O 6 HOH B 24 324 33 HOH HOH . O 6 HOH B 25 325 32 HOH HOH . O 6 HOH B 26 326 37 HOH HOH . O 6 HOH B 27 327 44 HOH HOH . O 6 HOH B 28 328 39 HOH HOH . O 6 HOH B 29 329 95 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 . . . I 3 22.902 5.3 24.302 1 18.81 ? PG GNP 202 B 1 HETATM 2 O O1G GNP . . . I 3 21.767 4.43 24.749 1 15.61 ? O1G GNP 202 B 1 HETATM 3 O O2G GNP . . . I 3 24.066 4.435 23.873 1 21.66 ? O2G GNP 202 B 1 HETATM 4 O O3G GNP . . . I 3 22.42 6.212 23.13 1 20.22 ? O3G GNP 202 B 1 HETATM 5 N N3B GNP . . . I 3 23.488 6.305 25.549 1 17.82 ? N3B GNP 202 B 1 HETATM 6 P PB GNP . . . I 3 22.462 7.208 26.441 1 22.06 ? PB GNP 202 B 1 HETATM 7 O O1B GNP . . . I 3 21.134 6.509 26.401 1 17.43 ? O1B GNP 202 B 1 HETATM 8 O O2B GNP . . . I 3 22.339 8.601 25.912 1 19.69 ? O2B GNP 202 B 1 HETATM 9 O O3A GNP . . . I 3 23.081 7.34 27.963 1 20.28 ? O3A GNP 202 B 1 HETATM 10 P PA GNP . . . I 3 22.617 6.639 29.313 1 20 ? PA GNP 202 B 1 HETATM 11 O O1A GNP . . . I 3 22.578 5.127 29.091 1 11.99 ? O1A GNP 202 B 1 HETATM 12 O O2A GNP . . . I 3 21.394 7.24 29.859 1 17.31 ? O2A GNP 202 B 1 HETATM 13 O O5' GNP . . . I 3 23.754 7.076 30.305 1 17.43 ? O5' GNP 202 B 1 HETATM 14 C C5' GNP . . . I 3 25.152 6.917 29.983 1 22.68 ? C5' GNP 202 B 1 HETATM 15 C C4' GNP . . . I 3 25.965 6.861 31.267 1 14.59 ? C4' GNP 202 B 1 HETATM 16 O O4' GNP . . . I 3 26.043 8.176 31.866 1 10.41 ? O4' GNP 202 B 1 HETATM 17 C C3' GNP . . . I 3 25.428 5.942 32.362 1 20.68 ? C3' GNP 202 B 1 HETATM 18 O O3' GNP . . . I 3 26.524 5.339 33.037 1 20.79 ? O3' GNP 202 B 1 HETATM 19 C C2' GNP . . . I 3 24.622 6.908 33.237 1 16.42 ? C2' GNP 202 B 1 HETATM 20 O O2' GNP . . . I 3 24.462 6.52 34.594 1 17.61 ? O2' GNP 202 B 1 HETATM 21 C C1' GNP . . . I 3 25.503 8.152 33.173 1 17.28 ? C1' GNP 202 B 1 HETATM 22 N N9 GNP . . . I 3 24.746 9.394 33.369 1 16.32 ? N9 GNP 202 B 1 HETATM 23 C C8 GNP . . . I 3 23.693 9.803 32.613 1 15.22 ? C8 GNP 202 B 1 HETATM 24 N N7 GNP . . . I 3 23.215 10.965 32.992 1 18.79 ? N7 GNP 202 B 1 HETATM 25 C C5 GNP . . . I 3 24.016 11.326 34.048 1 11.68 ? C5 GNP 202 B 1 HETATM 26 C C6 GNP . . . I 3 23.985 12.511 34.891 1 17.46 ? C6 GNP 202 B 1 HETATM 27 O O6 GNP . . . I 3 23.2 13.437 34.799 1 15.72 ? O6 GNP 202 B 1 HETATM 28 N N1 GNP . . . I 3 24.964 12.482 35.855 1 15.96 ? N1 GNP 202 B 1 HETATM 29 C C2 GNP . . . I 3 25.874 11.472 36.027 1 20.23 ? C2 GNP 202 B 1 HETATM 30 N N2 GNP . . . I 3 26.763 11.61 37.008 1 30.03 ? N2 GNP 202 B 1 HETATM 31 N N3 GNP . . . I 3 25.909 10.387 35.247 1 24.83 ? N3 GNP 202 B 1 HETATM 32 C C4 GNP . . . I 3 24.961 10.384 34.312 1 17.61 ? C4 GNP 202 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #