data_8Y9F # _model_server_result.job_id PBnd9_qal7yIZhPj7GqWIA _model_server_result.datetime_utc '2024-12-01 01:27:02' _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 8y9f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":601}' # _entry.id 8Y9F # _exptl.entry_id 8Y9F _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 8Y9F _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y9F _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 _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 H N N ? 6 J 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 ASP 39 B ASP 39 1_555 A N ALY 40 B ALY 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C ALY 40 B ALY 40 1_555 A N SER 41 B SER 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _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 111 n n PG O2G G2P doub 112 n n PG O3G G2P sing 113 n n PG O3B G2P sing 114 n n O3B PB G2P sing 115 n n PB O1B G2P sing 116 n n PB O2B G2P doub 117 n n PB C3A G2P sing 118 n n C3A PA G2P sing 119 n n C3A H3A1 G2P sing 120 n n C3A H3A2 G2P sing 121 n n PA O1A G2P sing 122 n n PA O2A G2P doub 123 n n PA O5' G2P sing 124 n n O5' C5' G2P sing 125 n n C5' C4' G2P sing 126 n n C5' "H5'1" G2P sing 127 n n C5' "H5'2" G2P sing 128 n n C4' O4' G2P sing 129 n n C4' C3' G2P sing 130 n n C4' H4' G2P sing 131 n n O4' C1' G2P sing 132 n n C3' O3' G2P sing 133 n n C3' C2' G2P sing 134 n n C3' H3' G2P sing 135 n n O3' HA G2P sing 136 n n C2' O2' G2P sing 137 n n C2' C1' G2P sing 138 n n C2' H2' G2P sing 139 n n O2' HB G2P sing 140 n n C1' N9 G2P sing 141 n n C1' H1' G2P sing 142 n n N9 C8 G2P sing 143 n y N9 C4 G2P sing 144 n y C8 N7 G2P doub 145 n y C8 H8 G2P sing 146 n n N7 C5 G2P sing 147 n y C5 C6 G2P sing 148 n y C5 C4 G2P doub 149 n y C6 O6 G2P doub 150 n n C6 N1 G2P sing 151 n y N1 C2 G2P sing 152 n y N1 H1 G2P sing 153 n n C2 N2 G2P sing 154 n n C2 N3 G2P doub 155 n y N2 H2N1 G2P sing 156 n n N2 H2N2 G2P sing 157 n n N3 C4 G2P sing 158 n y HO1 O1G G2P sing 159 n n HO2 O3G G2P sing 160 n n HO3 O1A G2P sing 161 n n HO4 O1B G2P sing 162 n n # _atom_sites.entry_id 8Y9F _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 5 GTP B 1 501 603 GTP GTP . H 6 G2P D 1 601 601 G2P G2P . I 5 GTP E 1 501 604 GTP GTP . J 6 G2P F 1 601 601 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 . . . J 6 137.09 239.593 230.543 1 69.69 ? PG G2P 601 F 1 HETATM 2 O O1G G2P . . . J 6 137.64 240.716 229.727 1 69.69 ? O1G G2P 601 F 1 HETATM 3 O O2G G2P . . . J 6 138.141 238.57 230.883 1 69.69 ? O2G G2P 601 F 1 HETATM 4 O O3G G2P . . . J 6 135.865 238.99 229.938 1 69.69 ? O3G G2P 601 F 1 HETATM 5 O O3B G2P . . . J 6 136.579 240.254 231.899 1 69.69 ? O3B G2P 601 F 1 HETATM 6 P PB G2P . . . J 6 137.453 240.852 233.059 1 69.69 ? PB G2P 601 F 1 HETATM 7 O O1B G2P . . . J 6 136.659 241.061 234.308 1 69.69 ? O1B G2P 601 F 1 HETATM 8 O O2B G2P . . . J 6 138.688 240.021 233.181 1 69.69 ? O2B G2P 601 F 1 HETATM 9 C C3A G2P . . . J 6 137.924 242.442 232.391 1 69.69 ? C3A G2P 601 F 1 HETATM 10 P PA G2P . . . J 6 139.125 243.145 233.491 1 69.69 ? PA G2P 601 F 1 HETATM 11 O O1A G2P . . . J 6 139.354 242.179 234.606 1 69.69 ? O1A G2P 601 F 1 HETATM 12 O O2A G2P . . . J 6 140.319 243.485 232.664 1 69.69 ? O2A G2P 601 F 1 HETATM 13 O O5' G2P . . . J 6 138.51 244.482 234.044 1 69.69 ? O5' G2P 601 F 1 HETATM 14 C C5' G2P . . . J 6 138.646 245.719 233.321 1 69.69 ? C5' G2P 601 F 1 HETATM 15 C C4' G2P . . . J 6 139.638 246.589 234.044 1 69.69 ? C4' G2P 601 F 1 HETATM 16 O O4' G2P . . . J 6 140.661 245.754 234.618 1 69.69 ? O4' G2P 601 F 1 HETATM 17 C C3' G2P . . . J 6 140.428 247.584 233.186 1 69.69 ? C3' G2P 601 F 1 HETATM 18 O O3' G2P . . . J 6 139.876 248.883 233.338 1 69.69 ? O3' G2P 601 F 1 HETATM 19 C C2' G2P . . . J 6 141.856 247.521 233.745 1 69.69 ? C2' G2P 601 F 1 HETATM 20 O O2' G2P . . . J 6 142.315 248.797 234.125 1 69.69 ? O2' G2P 601 F 1 HETATM 21 C C1' G2P . . . J 6 141.714 246.612 234.957 1 69.69 ? C1' G2P 601 F 1 HETATM 22 N N9 G2P . . . J 6 142.879 245.79 235.235 1 69.69 ? N9 G2P 601 F 1 HETATM 23 C C8 G2P . . . J 6 143.376 244.78 234.457 1 69.69 ? C8 G2P 601 F 1 HETATM 24 N N7 G2P . . . J 6 144.419 244.192 234.984 1 69.69 ? N7 G2P 601 F 1 HETATM 25 C C5 G2P . . . J 6 144.599 244.838 236.196 1 69.69 ? C5 G2P 601 F 1 HETATM 26 C C6 G2P . . . J 6 145.566 244.628 237.204 1 69.69 ? C6 G2P 601 F 1 HETATM 27 O O6 G2P . . . J 6 146.474 243.792 237.235 1 69.69 ? O6 G2P 601 F 1 HETATM 28 N N1 G2P . . . J 6 145.386 245.499 238.272 1 69.69 ? N1 G2P 601 F 1 HETATM 29 C C2 G2P . . . J 6 144.415 246.459 238.355 1 69.69 ? C2 G2P 601 F 1 HETATM 30 N N2 G2P . . . J 6 144.412 247.202 239.466 1 69.69 ? N2 G2P 601 F 1 HETATM 31 N N3 G2P . . . J 6 143.503 246.663 237.411 1 69.69 ? N3 G2P 601 F 1 HETATM 32 C C4 G2P . . . J 6 143.656 245.821 236.365 1 69.69 ? C4 G2P 601 F 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #