data_3RYT # _model_server_result.job_id Agd_2tqFE-5auIwEanFsGA _model_server_result.datetime_utc '2024-12-21 08:29:16' _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 3ryt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":179}' # _entry.id 3RYT # _exptl.entry_id 3RYT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 4 _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 3RYT _cell.length_a 110.783 _cell.length_b 110.783 _cell.length_c 265.628 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RYT _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 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 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,E 1 1 B 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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 C OG1 THR 20 C THR 17 1_555 D MG MG . C MG 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc2 C OD1 ASP 60 C ASP 57 1_555 D MG MG . C MG 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? metalc ? metalc3 D MG MG . C MG 178 1_555 E O2B GNP . C GNP 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? metalc ? metalc4 D MG MG . C MG 178 1_555 E O1G GNP . C GNP 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc5 D MG MG . C MG 178 1_555 E O2G GNP . C GNP 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? # _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 3RYT _atom_sites.fract_transf_matrix[1][1] 0.009027 _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] 0.009027 _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] 0.003765 _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 D 3 MG C 1 178 1 MG MG . E 4 GNP C 1 179 2 GNP GNP . # 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 . . . E 4 -63.49 -58.312 -12.962 1 144.64 ? PG GNP 179 C 1 HETATM 2 O O1G GNP . . . E 4 -62.565 -58.326 -14.154 1 144.02 ? O1G GNP 179 C 1 HETATM 3 O O2G GNP . . . E 4 -62.902 -57.769 -11.681 1 140.14 ? O2G GNP 179 C 1 HETATM 4 O O3G GNP . . . E 4 -64.739 -57.631 -13.465 1 141.64 ? O3G GNP 179 C 1 HETATM 5 N N3B GNP . . . E 4 -63.923 -59.798 -12.634 1 392.15 ? N3B GNP 179 C 1 HETATM 6 P PB GNP . . . E 4 -62.829 -60.9 -12.33 1 143.57 ? PB GNP 179 C 1 HETATM 7 O O1B GNP . . . E 4 -62.291 -61.449 -13.594 1 126.31 ? O1B GNP 179 C 1 HETATM 8 O O2B GNP . . . E 4 -61.886 -60.269 -11.381 1 160.98 ? O2B GNP 179 C 1 HETATM 9 O O3A GNP . . . E 4 -63.496 -62.058 -11.603 1 149.01 ? O3A GNP 179 C 1 HETATM 10 P PA GNP . . . E 4 -63.093 -62.401 -10.179 1 155.29 ? PA GNP 179 C 1 HETATM 11 O O1A GNP . . . E 4 -61.748 -63.015 -10.238 1 154.25 ? O1A GNP 179 C 1 HETATM 12 O O2A GNP . . . E 4 -63.281 -61.219 -9.309 1 153.82 ? O2A GNP 179 C 1 HETATM 13 O O5' GNP . . . E 4 -64.075 -63.513 -9.646 1 164.13 ? O5' GNP 179 C 1 HETATM 14 C C5' GNP . . . E 4 -65.475 -63.381 -9.832 1 165.24 ? C5' GNP 179 C 1 HETATM 15 C C4' GNP . . . E 4 -66.178 -64.581 -9.231 1 165.08 ? C4' GNP 179 C 1 HETATM 16 O O4' GNP . . . E 4 -65.713 -65.771 -9.91 1 167.17 ? O4' GNP 179 C 1 HETATM 17 C C3' GNP . . . E 4 -65.908 -64.784 -7.744 1 166.07 ? C3' GNP 179 C 1 HETATM 18 O O3' GNP . . . E 4 -67.124 -64.69 -7.004 1 162.36 ? O3' GNP 179 C 1 HETATM 19 C C2' GNP . . . E 4 -65.289 -66.177 -7.625 1 173.12 ? C2' GNP 179 C 1 HETATM 20 O O2' GNP . . . E 4 -65.901 -66.932 -6.596 1 179.42 ? O2' GNP 179 C 1 HETATM 21 C C1' GNP . . . E 4 -65.55 -66.822 -8.985 1 171.49 ? C1' GNP 179 C 1 HETATM 22 N N9 GNP . . . E 4 -64.447 -67.65 -9.463 1 174.4 ? N9 GNP 179 C 1 HETATM 23 C C8 GNP . . . E 4 -63.365 -67.228 -10.195 1 181.45 ? C8 GNP 179 C 1 HETATM 24 N N7 GNP . . . E 4 -62.528 -68.182 -10.49 1 181.2 ? N7 GNP 179 C 1 HETATM 25 C C5 GNP . . . E 4 -63.091 -69.311 -9.915 1 172.91 ? C5 GNP 179 C 1 HETATM 26 C C6 GNP . . . E 4 -62.631 -70.647 -9.905 1 170.74 ? C6 GNP 179 C 1 HETATM 27 O O6 GNP . . . E 4 -61.601 -71.103 -10.419 1 165.02 ? O6 GNP 179 C 1 HETATM 28 N N1 GNP . . . E 4 -63.499 -71.484 -9.21 1 177.06 ? N1 GNP 179 C 1 HETATM 29 C C2 GNP . . . E 4 -64.665 -71.078 -8.604 1 178.78 ? C2 GNP 179 C 1 HETATM 30 N N2 GNP . . . E 4 -65.374 -72.03 -7.98 1 184.53 ? N2 GNP 179 C 1 HETATM 31 N N3 GNP . . . E 4 -65.108 -69.828 -8.608 1 172.36 ? N3 GNP 179 C 1 HETATM 32 C C4 GNP . . . E 4 -64.273 -69.002 -9.28 1 170.85 ? C4 GNP 179 C 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #