data_2Q3F # _model_server_result.job_id MspUhIhtRjHKnhWJ9oS3-A _model_server_result.datetime_utc '2025-03-31 03:25:08' _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 2q3f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 2Q3F # _exptl.entry_id 2Q3F _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 110.92 _cell.angle_gamma 90 _cell.entry_id 2Q3F _cell.length_a 47.73 _cell.length_b 67.13 _cell.length_c 66.36 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Q3F _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 D N N ? 3 F 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 covale ? covale1 A C LEU 9 A LEU 48 1_555 A N MSE 10 A MSE 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C MSE 10 A MSE 49 1_555 A N GLY 11 A GLY 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C LYS 27 A LYS 66 1_555 A N MSE 28 A MSE 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C MSE 28 A MSE 67 1_555 A N SER 29 A SER 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 A C GLU 74 A GLU 113 1_555 A N MSE 75 A MSE 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 A C MSE 75 A MSE 114 1_555 A N ILE 76 A ILE 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 A C TYR 93 A TYR 132 1_555 A N MSE 94 A MSE 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 A C MSE 94 A MSE 133 1_555 A N GLU 95 A GLU 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale9 B C LEU 9 B LEU 48 1_555 B N MSE 10 B MSE 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 B C MSE 10 B MSE 49 1_555 B N GLY 11 B GLY 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 B C LYS 27 B LYS 66 1_555 B N MSE 28 B MSE 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale12 B C MSE 28 B MSE 67 1_555 B N SER 29 B SER 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale13 B C GLU 74 B GLU 113 1_555 B N MSE 75 B MSE 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale14 B C MSE 75 B MSE 114 1_555 B N ILE 76 B ILE 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale15 B C TYR 93 B TYR 132 1_555 B N MSE 94 B MSE 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale16 B C MSE 94 B MSE 133 1_555 B N GLU 95 B GLU 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A OG SER 18 A SER 57 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc2 A OG1 THR 39 A THR 78 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc3 C MG MG . A MG 301 1_555 D O1G GNP . A GNP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc4 C MG MG . A MG 301 1_555 D O2B GNP . A GNP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc5 C MG MG . A MG 301 1_555 G O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc6 C MG MG . A MG 301 1_555 G O HOH . A HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc7 B OG SER 18 B SER 57 1_555 E MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc8 B OG1 THR 39 B THR 78 1_555 E MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc9 E MG MG . B MG 302 1_555 F O2B GNP . B GNP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc10 E MG MG . B MG 302 1_555 F O1G GNP . B GNP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc11 E MG MG . B MG 302 1_555 H O HOH . B HOH 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc12 E MG MG . B MG 302 1_555 H O HOH . B HOH 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? # _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 2Q3F _atom_sites.fract_transf_matrix[1][1] 0.020951 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008009 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014896 _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] 0.016133 _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 MG A 1 301 301 MG MG . D 3 GNP A 1 401 401 GNP GNP . E 2 MG B 1 302 302 MG MG . F 3 GNP B 1 402 402 GNP GNP . G 4 HOH A 1 402 2 HOH HOH . G 4 HOH A 2 403 7 HOH HOH . G 4 HOH A 3 404 9 HOH HOH . G 4 HOH A 4 405 10 HOH HOH . G 4 HOH A 5 406 13 HOH HOH . G 4 HOH A 6 407 14 HOH HOH . G 4 HOH A 7 408 17 HOH HOH . G 4 HOH A 8 409 18 HOH HOH . G 4 HOH A 9 410 20 HOH HOH . G 4 HOH A 10 411 24 HOH HOH . G 4 HOH A 11 412 26 HOH HOH . G 4 HOH A 12 413 30 HOH HOH . G 4 HOH A 13 414 33 HOH HOH . G 4 HOH A 14 415 34 HOH HOH . G 4 HOH A 15 416 35 HOH HOH . G 4 HOH A 16 417 37 HOH HOH . G 4 HOH A 17 418 40 HOH HOH . G 4 HOH A 18 419 41 HOH HOH . G 4 HOH A 19 420 42 HOH HOH . G 4 HOH A 20 421 44 HOH HOH . G 4 HOH A 21 422 50 HOH HOH . G 4 HOH A 22 423 53 HOH HOH . G 4 HOH A 23 424 55 HOH HOH . G 4 HOH A 24 425 56 HOH HOH . G 4 HOH A 25 426 57 HOH HOH . G 4 HOH A 26 427 64 HOH HOH . G 4 HOH A 27 428 66 HOH HOH . G 4 HOH A 28 429 72 HOH HOH . G 4 HOH A 29 430 73 HOH HOH . G 4 HOH A 30 431 74 HOH HOH . G 4 HOH A 31 432 75 HOH HOH . G 4 HOH A 32 433 82 HOH HOH . G 4 HOH A 33 434 84 HOH HOH . G 4 HOH A 34 435 87 HOH HOH . G 4 HOH A 35 436 93 HOH HOH . G 4 HOH A 36 437 94 HOH HOH . G 4 HOH A 37 438 98 HOH HOH . G 4 HOH A 38 439 99 HOH HOH . G 4 HOH A 39 440 100 HOH HOH . G 4 HOH A 40 441 106 HOH HOH . G 4 HOH A 41 442 107 HOH HOH . G 4 HOH A 42 443 108 HOH HOH . G 4 HOH A 43 444 110 HOH HOH . H 4 HOH B 1 403 1 HOH HOH . H 4 HOH B 2 404 3 HOH HOH . H 4 HOH B 3 405 4 HOH HOH . H 4 HOH B 4 406 5 HOH HOH . H 4 HOH B 5 407 8 HOH HOH . H 4 HOH B 6 408 11 HOH HOH . H 4 HOH B 7 409 12 HOH HOH . H 4 HOH B 8 410 15 HOH HOH . H 4 HOH B 9 411 16 HOH HOH . H 4 HOH B 10 412 19 HOH HOH . H 4 HOH B 11 413 21 HOH HOH . H 4 HOH B 12 414 23 HOH HOH . H 4 HOH B 13 415 25 HOH HOH . H 4 HOH B 14 416 27 HOH HOH . H 4 HOH B 15 417 28 HOH HOH . H 4 HOH B 16 418 32 HOH HOH . H 4 HOH B 17 419 39 HOH HOH . H 4 HOH B 18 420 43 HOH HOH . H 4 HOH B 19 421 46 HOH HOH . H 4 HOH B 20 422 47 HOH HOH . H 4 HOH B 21 423 51 HOH HOH . H 4 HOH B 22 424 52 HOH HOH . H 4 HOH B 23 425 54 HOH HOH . H 4 HOH B 24 426 59 HOH HOH . H 4 HOH B 25 427 60 HOH HOH . H 4 HOH B 26 428 63 HOH HOH . H 4 HOH B 27 429 65 HOH HOH . H 4 HOH B 28 430 67 HOH HOH . H 4 HOH B 29 431 71 HOH HOH . H 4 HOH B 30 432 76 HOH HOH . H 4 HOH B 31 433 78 HOH HOH . H 4 HOH B 32 434 80 HOH HOH . H 4 HOH B 33 435 83 HOH HOH . H 4 HOH B 34 436 85 HOH HOH . H 4 HOH B 35 437 86 HOH HOH . H 4 HOH B 36 438 88 HOH HOH . H 4 HOH B 37 439 89 HOH HOH . H 4 HOH B 38 440 90 HOH HOH . H 4 HOH B 39 441 91 HOH HOH . H 4 HOH B 40 442 92 HOH HOH . H 4 HOH B 41 443 95 HOH HOH . H 4 HOH B 42 444 97 HOH HOH . H 4 HOH B 43 445 101 HOH HOH . H 4 HOH B 44 446 102 HOH HOH . H 4 HOH B 45 447 104 HOH HOH . H 4 HOH B 46 448 105 HOH HOH . H 4 HOH B 47 449 109 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 . . . F 3 34.042 32.877 34.823 1 30.2 ? PG GNP 402 B 1 HETATM 2 O O1G GNP . . . F 3 32.895 32.177 34.202 1 29.28 ? O1G GNP 402 B 1 HETATM 3 O O2G GNP . . . F 3 34.631 33.924 33.96 1 32.45 ? O2G GNP 402 B 1 HETATM 4 O O3G GNP . . . F 3 33.789 33.32 36.213 1 27.82 ? O3G GNP 402 B 1 HETATM 5 N N3B GNP . . . F 3 35.269 31.674 34.962 1 26.99 ? N3B GNP 402 B 1 HETATM 6 P PB GNP . . . F 3 35.092 30.141 35.728 1 25.85 ? PB GNP 402 B 1 HETATM 7 O O1B GNP . . . F 3 35.174 30.53 37.268 1 26.75 ? O1B GNP 402 B 1 HETATM 8 O O2B GNP . . . F 3 33.828 29.5 35.276 1 25.99 ? O2B GNP 402 B 1 HETATM 9 O O3A GNP . . . F 3 36.397 29.379 35.245 1 29.06 ? O3A GNP 402 B 1 HETATM 10 P PA GNP . . . F 3 36.316 28.282 34.091 1 30.17 ? PA GNP 402 B 1 HETATM 11 O O1A GNP . . . F 3 35.408 27.189 34.513 1 31.46 ? O1A GNP 402 B 1 HETATM 12 O O2A GNP . . . F 3 36.057 28.994 32.819 1 30.47 ? O2A GNP 402 B 1 HETATM 13 O O5' GNP . . . F 3 37.794 27.688 34.078 1 34.72 ? O5' GNP 402 B 1 HETATM 14 C C5' GNP . . . F 3 38.915 28.489 33.693 1 36.1 ? C5' GNP 402 B 1 HETATM 15 C C4' GNP . . . F 3 40.1 27.6 33.39 1 37.39 ? C4' GNP 402 B 1 HETATM 16 O O4' GNP . . . F 3 40.512 26.951 34.607 1 34.77 ? O4' GNP 402 B 1 HETATM 17 C C3' GNP . . . F 3 39.816 26.46 32.421 1 38.97 ? C3' GNP 402 B 1 HETATM 18 O O3' GNP . . . F 3 40.111 26.893 31.1 1 42.9 ? O3' GNP 402 B 1 HETATM 19 C C2' GNP . . . F 3 40.797 25.365 32.827 1 40.27 ? C2' GNP 402 B 1 HETATM 20 O O2' GNP . . . F 3 42.009 25.438 32.101 1 51.13 ? O2' GNP 402 B 1 HETATM 21 C C1' GNP . . . F 3 41.093 25.714 34.286 1 38.43 ? C1' GNP 402 B 1 HETATM 22 N N9 GNP . . . F 3 40.762 24.737 35.313 1 35.38 ? N9 GNP 402 B 1 HETATM 23 C C8 GNP . . . F 3 39.533 24.429 35.846 1 34.68 ? C8 GNP 402 B 1 HETATM 24 N N7 GNP . . . F 3 39.601 23.546 36.803 1 34.36 ? N7 GNP 402 B 1 HETATM 25 C C5 GNP . . . F 3 40.955 23.245 36.894 1 35.7 ? C5 GNP 402 B 1 HETATM 26 C C6 GNP . . . F 3 41.649 22.35 37.751 1 35.62 ? C6 GNP 402 B 1 HETATM 27 O O6 GNP . . . F 3 41.194 21.618 38.634 1 37.31 ? O6 GNP 402 B 1 HETATM 28 N N1 GNP . . . F 3 43.017 22.356 37.495 1 35.05 ? N1 GNP 402 B 1 HETATM 29 C C2 GNP . . . F 3 43.64 23.119 36.54 1 35.86 ? C2 GNP 402 B 1 HETATM 30 N N2 GNP . . . F 3 44.972 22.991 36.448 1 33.34 ? N2 GNP 402 B 1 HETATM 31 N N3 GNP . . . F 3 43.006 23.95 35.735 1 35.75 ? N3 GNP 402 B 1 HETATM 32 C C4 GNP . . . F 3 41.676 23.963 35.968 1 36.1 ? C4 GNP 402 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #