data_8YAJ # _model_server_result.job_id 6-RY7VsSilQ4uzZmjguVyA _model_server_result.datetime_utc '2024-11-28 08:53:26' _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 8yaj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 8YAJ # _exptl.entry_id 8YAJ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 521.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC 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 8YAJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YAJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 ? 6 I N N ? 6 K N N # _chem_comp.formula 'C11 H18 N5 O13 P3' _chem_comp.formula_weight 521.208 _chem_comp.id G2P _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC 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 G2P sing 83 n n PG O2G G2P doub 84 n n PG O3G G2P sing 85 n n PG O3B G2P sing 86 n n O3B PB G2P sing 87 n n PB O1B G2P sing 88 n n PB O2B G2P doub 89 n n PB C3A G2P sing 90 n n C3A PA G2P sing 91 n n C3A H3A1 G2P sing 92 n n C3A H3A2 G2P sing 93 n n PA O1A G2P sing 94 n n PA O2A G2P doub 95 n n PA O5' G2P sing 96 n n O5' C5' G2P sing 97 n n C5' C4' G2P sing 98 n n C5' "H5'1" G2P sing 99 n n C5' "H5'2" G2P sing 100 n n C4' O4' G2P sing 101 n n C4' C3' G2P sing 102 n n C4' H4' G2P sing 103 n n O4' C1' G2P sing 104 n n C3' O3' G2P sing 105 n n C3' C2' G2P sing 106 n n C3' H3' G2P sing 107 n n O3' HA G2P sing 108 n n C2' O2' G2P sing 109 n n C2' C1' G2P sing 110 n n C2' H2' G2P sing 111 n n O2' HB G2P sing 112 n n C1' N9 G2P sing 113 n n C1' H1' G2P sing 114 n n N9 C8 G2P sing 115 n y N9 C4 G2P sing 116 n y C8 N7 G2P doub 117 n y C8 H8 G2P sing 118 n n N7 C5 G2P sing 119 n y C5 C6 G2P sing 120 n y C5 C4 G2P doub 121 n y C6 O6 G2P doub 122 n n C6 N1 G2P sing 123 n y N1 C2 G2P sing 124 n y N1 H1 G2P sing 125 n n C2 N2 G2P sing 126 n n C2 N3 G2P doub 127 n y N2 H2N1 G2P sing 128 n n N2 H2N2 G2P sing 129 n n N3 C4 G2P sing 130 n y HO1 O1G G2P sing 131 n n HO2 O3G G2P sing 132 n n HO3 O1A G2P sing 133 n n HO4 O1B G2P sing 134 n n # _atom_sites.entry_id 8YAJ _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 G 4 GTP B 1 501 501 GTP GTP . H 5 PIN C 1 301 201 PIN PIN . I 6 G2P D 1 501 501 G2P G2P . J 4 GTP E 1 501 501 GTP GTP . K 6 G2P F 1 501 501 G2P G2P . # 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 G2P . . . K 6 136.539 239.611 230.668 1 74.16 ? PG G2P 501 F 1 HETATM 2 O O1G G2P . . . K 6 135.393 238.662 230.364 1 74.16 ? O1G G2P 501 F 1 HETATM 3 O O2G G2P . . . K 6 136.518 240.877 229.813 1 74.16 ? O2G G2P 501 F 1 HETATM 4 O O3G G2P . . . K 6 137.878 238.936 230.771 1 74.16 ? O3G G2P 501 F 1 HETATM 5 O O3B G2P . . . K 6 136.252 240.219 232.21 1 74.16 ? O3B G2P 501 F 1 HETATM 6 P PB G2P . . . K 6 137.149 240.579 233.414 1 74.16 ? PB G2P 501 F 1 HETATM 7 O O1B G2P . . . K 6 136.421 241.12 234.619 1 74.16 ? O1B G2P 501 F 1 HETATM 8 O O2B G2P . . . K 6 138.224 239.58 233.685 1 74.16 ? O2B G2P 501 F 1 HETATM 9 C C3A G2P . . . K 6 138.06 242.126 232.765 1 74.16 ? C3A G2P 501 F 1 HETATM 10 P PA G2P . . . K 6 139.466 242.632 233.484 1 74.16 ? PA G2P 501 F 1 HETATM 11 O O1A G2P . . . K 6 140.034 241.854 234.637 1 74.16 ? O1A G2P 501 F 1 HETATM 12 O O2A G2P . . . K 6 140.539 243.134 232.553 1 74.16 ? O2A G2P 501 F 1 HETATM 13 O O5' G2P . . . K 6 139.071 244.155 234.265 1 74.16 ? O5' G2P 501 F 1 HETATM 14 C C5' G2P . . . K 6 138.876 245.272 233.559 1 74.16 ? C5' G2P 501 F 1 HETATM 15 C C4' G2P . . . K 6 139.544 246.428 234.357 1 74.16 ? C4' G2P 501 F 1 HETATM 16 O O4' G2P . . . K 6 140.546 245.89 235.189 1 74.16 ? O4' G2P 501 F 1 HETATM 17 C C3' G2P . . . K 6 140.236 247.457 233.425 1 74.16 ? C3' G2P 501 F 1 HETATM 18 O O3' G2P . . . K 6 140.042 248.751 233.916 1 74.16 ? O3' G2P 501 F 1 HETATM 19 C C2' G2P . . . K 6 141.728 247.108 233.59 1 74.16 ? C2' G2P 501 F 1 HETATM 20 O O2' G2P . . . K 6 142.583 248.19 233.43 1 74.16 ? O2' G2P 501 F 1 HETATM 21 C C1' G2P . . . K 6 141.7 246.645 235.067 1 74.16 ? C1' G2P 501 F 1 HETATM 22 N N9 G2P . . . K 6 142.84 245.761 235.335 1 74.16 ? N9 G2P 501 F 1 HETATM 23 C C8 G2P . . . K 6 143.343 244.722 234.542 1 74.16 ? C8 G2P 501 F 1 HETATM 24 N N7 G2P . . . K 6 144.402 244.12 235.105 1 74.16 ? N7 G2P 501 F 1 HETATM 25 C C5 G2P . . . K 6 144.561 244.812 236.292 1 74.16 ? C5 G2P 501 F 1 HETATM 26 C C6 G2P . . . K 6 145.582 244.536 237.263 1 74.16 ? C6 G2P 501 F 1 HETATM 27 O O6 G2P . . . K 6 146.451 243.714 237.262 1 74.16 ? O6 G2P 501 F 1 HETATM 28 N N1 G2P . . . K 6 145.434 245.446 238.348 1 74.16 ? N1 G2P 501 F 1 HETATM 29 C C2 G2P . . . K 6 144.455 246.428 238.427 1 74.16 ? C2 G2P 501 F 1 HETATM 30 N N2 G2P . . . K 6 144.466 247.225 239.563 1 74.16 ? N2 G2P 501 F 1 HETATM 31 N N3 G2P . . . K 6 143.502 246.694 237.534 1 74.16 ? N3 G2P 501 F 1 HETATM 32 C C4 G2P . . . K 6 143.611 245.819 236.446 1 74.16 ? C4 G2P 501 F 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 122 _model_server_stats.query_time_ms 584 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #