data_4YDH # _model_server_result.job_id fkcffskM5D3-P0tOQds4Jg _model_server_result.datetime_utc '2024-11-25 20:56:40' _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 4ydh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 4YDH # _exptl.entry_id 4YDH _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 4YDH _cell.length_a 87.6 _cell.length_b 102.1 _cell.length_c 170.6 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YDH _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 PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 G 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 B OG1 THR 19 B THR 17 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc2 B OG1 THR 37 B THR 35 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc3 E O2G GNP . B GNP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc4 E O2B GNP . B GNP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc5 D OG1 THR 19 D THR 17 1_555 H MG MG . D MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc6 D OG1 THR 37 D THR 35 1_555 H MG MG . D MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc7 D OD2 ASP 59 D ASP 57 1_555 H MG MG . D MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc8 G O1G GNP . D GNP 201 1_555 H MG MG . D MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc9 G O1B GNP . D GNP 201 1_555 H MG MG . D MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? # _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 4YDH _atom_sites.fract_transf_matrix[1][1] 0.011416 _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] 0.009794 _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] 0.005862 _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 E 3 GNP B 1 201 201 GNP GNP . F 4 MG B 1 202 202 MG MG . G 3 GNP D 1 201 201 GNP GNP . H 4 MG D 1 202 202 MG MG . # 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 3 34.398 25.593 75.107 1 10.62 ? PG GNP 201 B 1 HETATM 2 O O1G GNP . . . E 3 33.634 24.846 74.028 1 12.39 ? O1G GNP 201 B 1 HETATM 3 O O2G GNP . . . E 3 34.914 24.61 76.163 1 9.21 ? O2G GNP 201 B 1 HETATM 4 O O3G GNP . . . E 3 33.576 26.732 75.651 1 11.54 ? O3G GNP 201 B 1 HETATM 5 N N3B GNP . . . E 3 35.705 26.287 74.246 1 8.84 ? N3B GNP 201 B 1 HETATM 6 P PB GNP . . . E 3 36.991 27.029 75.078 1 8.16 ? PB GNP 201 B 1 HETATM 7 O O1B GNP . . . E 3 36.678 28.491 75.186 1 7.9 ? O1B GNP 201 B 1 HETATM 8 O O2B GNP . . . E 3 37.364 26.33 76.378 1 8.41 ? O2B GNP 201 B 1 HETATM 9 O O3A GNP . . . E 3 38.146 26.845 73.979 1 8.77 ? O3A GNP 201 B 1 HETATM 10 P PA GNP . . . E 3 39.464 25.925 74.034 1 8.96 ? PA GNP 201 B 1 HETATM 11 O O1A GNP . . . E 3 38.938 24.493 74.016 1 10.35 ? O1A GNP 201 B 1 HETATM 12 O O2A GNP . . . E 3 40.4 26.28 75.084 1 8.73 ? O2A GNP 201 B 1 HETATM 13 O O5' GNP . . . E 3 40.154 26.294 72.637 1 9.21 ? O5' GNP 201 B 1 HETATM 14 C C5' GNP . . . E 3 39.413 26.027 71.371 1 12.02 ? C5' GNP 201 B 1 HETATM 15 C C4' GNP . . . E 3 40.486 25.812 70.232 1 11.58 ? C4' GNP 201 B 1 HETATM 16 O O4' GNP . . . E 3 41.274 27.025 70.144 1 11.64 ? O4' GNP 201 B 1 HETATM 17 C C3' GNP . . . E 3 41.367 24.734 70.667 1 12.4 ? C3' GNP 201 B 1 HETATM 18 O O3' GNP . . . E 3 41.733 23.863 69.521 1 15.23 ? O3' GNP 201 B 1 HETATM 19 C C2' GNP . . . E 3 42.686 25.332 71.153 1 12.67 ? C2' GNP 201 B 1 HETATM 20 O O2' GNP . . . E 3 43.891 24.699 70.79 1 13.1 ? O2' GNP 201 B 1 HETATM 21 C C1' GNP . . . E 3 42.603 26.712 70.439 1 11.61 ? C1' GNP 201 B 1 HETATM 22 N N9 GNP . . . E 3 43.213 27.832 71.111 1 11.29 ? N9 GNP 201 B 1 HETATM 23 C C8 GNP . . . E 3 42.959 28.222 72.431 1 9.7 ? C8 GNP 201 B 1 HETATM 24 N N7 GNP . . . E 3 43.65 29.269 72.723 1 9.4 ? N7 GNP 201 B 1 HETATM 25 C C5 GNP . . . E 3 44.385 29.611 71.621 1 10.43 ? C5 GNP 201 B 1 HETATM 26 C C6 GNP . . . E 3 45.296 30.635 71.361 1 10.15 ? C6 GNP 201 B 1 HETATM 27 O O6 GNP . . . E 3 45.656 31.483 72.187 1 9.86 ? O6 GNP 201 B 1 HETATM 28 N N1 GNP . . . E 3 45.842 30.675 70.114 1 10.22 ? N1 GNP 201 B 1 HETATM 29 C C2 GNP . . . E 3 45.516 29.754 69.143 1 12.78 ? C2 GNP 201 B 1 HETATM 30 N N2 GNP . . . E 3 46.113 29.897 67.918 1 15.18 ? N2 GNP 201 B 1 HETATM 31 N N3 GNP . . . E 3 44.655 28.761 69.356 1 12.85 ? N3 GNP 201 B 1 HETATM 32 C C4 GNP . . . E 3 44.083 28.678 70.59 1 11.57 ? C4 GNP 201 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #