data_4ZU9 # _model_server_result.job_id jIRsfxqgI8_aCEGR40FXLg _model_server_result.datetime_utc '2025-01-02 17:27:22' _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 4zu9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2001}' # _entry.id 4ZU9 # _exptl.entry_id 4ZU9 _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 90 _cell.entry_id 4ZU9 _cell.length_a 114.24 _cell.length_b 114.24 _cell.length_c 204.632 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZU9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _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,G _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 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 covale ? covale1 A C MSE 1 A MSE 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C ILE 92 A ILE 92 1_555 A N MSE 93 A MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C MSE 93 A MSE 93 1_555 A N PRO 94 A PRO 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale4 A C LYS 117 A LYS 117 1_555 A N MSE 118 A MSE 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 A C MSE 118 A MSE 118 1_555 A N ASP 119 A ASP 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale6 A C GLU 141 A GLU 141 1_555 A N MSE 142 A MSE 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 A C MSE 142 A MSE 142 1_555 A N ASN 143 A ASN 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale8 A C ASN 143 A ASN 143 1_555 A N MSE 144 A MSE 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale9 A C MSE 144 A MSE 144 1_555 A N GLU 145 A GLU 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale10 A C LYS 225 A LYS 225 1_555 A N MSE 226 A MSE 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale11 A C MSE 226 A MSE 226 1_555 A N GLN 227 A GLN 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale12 A C GLY 291 A GLY 291 1_555 A N MSE 292 A MSE 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale13 A C MSE 292 A MSE 292 1_555 A N ARG 293 A ARG 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 A C SER 438 A SER 438 1_555 A N MSE 439 A MSE 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale15 A C MSE 439 A MSE 439 1_555 A N PHE 440 A PHE 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale16 A C LEU 481 A LEU 481 1_555 A N MSE 482 A MSE 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale17 A C MSE 482 A MSE 482 1_555 A N SER 483 A SER 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 A OG1 THR 17 A THR 17 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc2 A OG SER 40 A SER 40 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc3 B O1G GNP . A GNP 2001 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc4 B O2B GNP . A GNP 2001 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? # _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 4ZU9 _atom_sites.fract_transf_matrix[1][1] 0.008754 _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] 0.008754 _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] 0.004887 _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 2001 2001 GNP GNP . C 3 MG A 1 2002 2002 MG MG . D 4 SO4 A 1 2003 4001 SO4 SO4 . E 4 SO4 A 1 2004 4002 SO4 SO4 . F 4 SO4 A 1 2005 4003 SO4 SO4 . G 5 CYS A 1 2006 1001 CYS CYS . # 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 -14.384 20.904 26.289 1 130.51 ? PG GNP 2001 A 1 HETATM 2 O O1G GNP . . . B 2 -15.779 20.61 25.78 1 134.82 ? O1G GNP 2001 A 1 HETATM 3 O O2G GNP . . . B 2 -14.428 22.033 27.241 1 124.01 ? O2G GNP 2001 A 1 HETATM 4 O O3G GNP . . . B 2 -13.474 21.294 25.143 1 127.11 ? O3G GNP 2001 A 1 HETATM 5 N N3B GNP . . . B 2 -13.831 19.609 27.131 1 65.9 ? N3B GNP 2001 A 1 HETATM 6 P PB GNP . . . B 2 -14.542 19.266 28.479 1 128.86 ? PB GNP 2001 A 1 HETATM 7 O O1B GNP . . . B 2 -14.697 20.469 29.308 1 114.63 ? O1B GNP 2001 A 1 HETATM 8 O O2B GNP . . . B 2 -15.726 18.448 28.183 1 131.78 ? O2B GNP 2001 A 1 HETATM 9 O O3A GNP . . . B 2 -13.76 18.379 29.41 1 134.44 ? O3A GNP 2001 A 1 HETATM 10 P PA GNP . . . B 2 -13.65 16.888 29.168 1 131.79 ? PA GNP 2001 A 1 HETATM 11 O O1A GNP . . . B 2 -14.654 16.132 29.961 1 103.87 ? O1A GNP 2001 A 1 HETATM 12 O O2A GNP . . . B 2 -13.556 16.767 27.691 1 127.87 ? O2A GNP 2001 A 1 HETATM 13 O O5' GNP . . . B 2 -12.265 16.356 29.712 1 142.37 ? O5' GNP 2001 A 1 HETATM 14 C C5' GNP . . . B 2 -11.013 16.725 29.116 1 133.44 ? C5' GNP 2001 A 1 HETATM 15 C C4' GNP . . . B 2 -9.953 15.881 29.808 1 120.51 ? C4' GNP 2001 A 1 HETATM 16 O O4' GNP . . . B 2 -10.299 15.805 31.25 1 115.63 ? O4' GNP 2001 A 1 HETATM 17 C C3' GNP . . . B 2 -10.068 14.442 29.339 1 121.16 ? C3' GNP 2001 A 1 HETATM 18 O O3' GNP . . . B 2 -8.83 14.008 28.762 1 120.78 ? O3' GNP 2001 A 1 HETATM 19 C C2' GNP . . . B 2 -10.415 13.737 30.691 1 117.72 ? C2' GNP 2001 A 1 HETATM 20 O O2' GNP . . . B 2 -9.975 12.343 30.719 1 123.94 ? O2' GNP 2001 A 1 HETATM 21 C C1' GNP . . . B 2 -9.777 14.625 31.767 1 114.11 ? C1' GNP 2001 A 1 HETATM 22 N N9 GNP . . . B 2 -10.367 14.291 33.05 1 111.74 ? N9 GNP 2001 A 1 HETATM 23 C C8 GNP . . . B 2 -11.702 14.569 33.219 1 113.01 ? C8 GNP 2001 A 1 HETATM 24 N N7 GNP . . . B 2 -12.191 14.199 34.396 1 113.14 ? N7 GNP 2001 A 1 HETATM 25 C C5 GNP . . . B 2 -11.12 13.631 35.029 1 112.04 ? C5 GNP 2001 A 1 HETATM 26 C C6 GNP . . . B 2 -11.082 13.067 36.324 1 118.63 ? C6 GNP 2001 A 1 HETATM 27 O O6 GNP . . . B 2 -12.09 13.039 37.03 1 125.48 ? O6 GNP 2001 A 1 HETATM 28 N N1 GNP . . . B 2 -9.823 12.59 36.63 1 119.94 ? N1 GNP 2001 A 1 HETATM 29 C C2 GNP . . . B 2 -8.747 12.671 35.781 1 121.08 ? C2 GNP 2001 A 1 HETATM 30 N N2 GNP . . . B 2 -7.62 12.162 36.268 1 124.74 ? N2 GNP 2001 A 1 HETATM 31 N N3 GNP . . . B 2 -8.785 13.215 34.551 1 116.25 ? N3 GNP 2001 A 1 HETATM 32 C C4 GNP . . . B 2 -9.996 13.674 34.228 1 112.32 ? C4 GNP 2001 A 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 32 #