data_3JAT # _model_server_result.job_id ZkdMMDPvZL-e5VmVllZSLw _model_server_result.datetime_utc '2025-01-31 10:54:19' _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 3jat # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"EA","auth_seq_id":501}' # _entry.id 3JAT # _exptl.entry_id 3JAT _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 521.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _entity.pdbx_number_of_molecules 6 _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 3JAT _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JAT _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 dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA _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 ? _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 ? 5 O N N ? 5 S N N ? 5 W N N ? 5 AA N N ? 5 EA N N ? 5 IA 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 M O1B GTP . E GTP 501 1_555 N MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc2 M O1G GTP . E GTP 501 1_555 N MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc3 O O2B G2P . F G2P 501 1_555 P MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc4 O O1G G2P . F G2P 501 1_555 P MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc5 Q O1B GTP . J GTP 501 1_555 R MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.855 ? metalc ? metalc6 Q O3G GTP . J GTP 501 1_555 R MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc7 S O2B G2P . G G2P 501 1_555 T MG MG . G MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc8 S O2G G2P . G G2P 501 1_555 T MG MG . G MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc9 U O1B GTP . C GTP 501 1_555 V MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc10 U O1G GTP . C GTP 501 1_555 V MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc11 W O2B G2P . D G2P 501 1_555 X MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc12 W O1G G2P . D G2P 501 1_555 X MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? metalc ? metalc13 Y O1B GTP . L GTP 501 1_555 Z MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.883 ? metalc ? metalc14 Y O3G GTP . L GTP 501 1_555 Z MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc15 AA O2B G2P . I G2P 501 1_555 BA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc16 AA O1G G2P . I G2P 501 1_555 BA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc17 CA O1B GTP . A GTP 501 1_555 DA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? metalc ? metalc18 CA O1G GTP . A GTP 501 1_555 DA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc19 EA O2B G2P . B G2P 501 1_555 FA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc20 EA O1G G2P . B G2P 501 1_555 FA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc21 GA O1B GTP . K GTP 501 1_555 HA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.862 ? metalc ? metalc22 GA O3G GTP . K GTP 501 1_555 HA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc23 IA O2B G2P . H G2P 501 1_555 JA MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc24 IA O2G G2P . H G2P 501 1_555 JA MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? # _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 3JAT _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 M 3 GTP E 1 501 501 GTP GTP . N 4 MG E 1 502 502 MG MG . O 5 G2P F 1 501 501 G2P G2P . P 4 MG F 1 502 502 MG MG . Q 3 GTP J 1 501 501 GTP GTP . R 4 MG J 1 502 502 MG MG . S 5 G2P G 1 501 501 G2P G2P . T 4 MG G 1 502 502 MG MG . U 3 GTP C 1 501 501 GTP GTP . V 4 MG C 1 502 502 MG MG . W 5 G2P D 1 501 501 G2P G2P . X 4 MG D 1 502 502 MG MG . Y 3 GTP L 1 501 501 GTP GTP . Z 4 MG L 1 502 502 MG MG . AA 5 G2P I 1 501 501 G2P G2P . BA 4 MG I 1 502 502 MG MG . CA 3 GTP A 1 501 501 GTP GTP . DA 4 MG A 1 502 502 MG MG . EA 5 G2P B 1 501 501 G2P G2P . FA 4 MG B 1 502 502 MG MG . GA 3 GTP K 1 501 501 GTP GTP . HA 4 MG K 1 502 502 MG MG . IA 5 G2P H 1 501 501 G2P G2P . JA 4 MG H 1 502 502 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 G2P . . . EA 5 335.592 458.577 305.687 1 10.9 ? PG G2P 501 B 1 HETATM 2 O O1G G2P . . . EA 5 336.228 457.245 305.356 1 10.94 ? O1G G2P 501 B 1 HETATM 3 O O2G G2P . . . EA 5 336.379 459.772 305.225 1 10.98 ? O2G G2P 501 B 1 HETATM 4 O O3G G2P . . . EA 5 334.133 458.643 305.315 1 10.98 ? O3G G2P 501 B 1 HETATM 5 O O3B G2P . . . EA 5 335.571 458.735 307.289 1 10.78 ? O3B G2P 501 B 1 HETATM 6 P PB G2P . . . EA 5 336.318 457.663 308.216 1 10.73 ? PB G2P 501 B 1 HETATM 7 O O1B G2P . . . EA 5 336.072 457.992 309.632 1 10.82 ? O1B G2P 501 B 1 HETATM 8 O O2B G2P . . . EA 5 335.811 456.251 307.624 1 10.75 ? O2B G2P 501 B 1 HETATM 9 C C3A G2P . . . EA 5 338.098 457.869 307.995 1 10.73 ? C3A G2P 501 B 1 HETATM 10 P PA G2P . . . EA 5 338.991 456.432 308.653 1 10.78 ? PA G2P 501 B 1 HETATM 11 O O1A G2P . . . EA 5 338.433 456.04 309.967 1 10.81 ? O1A G2P 501 B 1 HETATM 12 O O2A G2P . . . EA 5 338.828 455.148 307.694 1 10.71 ? O2A G2P 501 B 1 HETATM 13 O O5' G2P . . . EA 5 340.502 456.875 308.99 1 10.89 ? O5' G2P 501 B 1 HETATM 14 C C5' G2P . . . EA 5 341.727 456.646 308.287 1 10.96 ? C5' G2P 501 B 1 HETATM 15 C C4' G2P . . . EA 5 342.739 457.181 309.297 1 10.93 ? C4' G2P 501 B 1 HETATM 16 O O4' G2P . . . EA 5 342.784 456.412 310.505 1 10.84 ? O4' G2P 501 B 1 HETATM 17 C C3' G2P . . . EA 5 344.201 457.027 308.915 1 10.96 ? C3' G2P 501 B 1 HETATM 18 O O3' G2P . . . EA 5 345.085 457.901 309.642 1 11.03 ? O3' G2P 501 B 1 HETATM 19 C C2' G2P . . . EA 5 344.421 455.536 309.091 1 10.82 ? C2' G2P 501 B 1 HETATM 20 O O2' G2P . . . EA 5 345.822 455.42 308.857 1 10.85 ? O2' G2P 501 B 1 HETATM 21 C C1' G2P . . . EA 5 343.866 455.449 310.504 1 10.76 ? C1' G2P 501 B 1 HETATM 22 N N9 G2P . . . EA 5 343.388 454.069 310.714 1 10.63 ? N9 G2P 501 B 1 HETATM 23 C C8 G2P . . . EA 5 342.566 453.327 309.956 1 10.61 ? C8 G2P 501 B 1 HETATM 24 N N7 G2P . . . EA 5 342.385 452.103 310.511 1 10.63 ? N7 G2P 501 B 1 HETATM 25 C C5 G2P . . . EA 5 343.091 452.048 311.644 1 10.57 ? C5 G2P 501 B 1 HETATM 26 C C6 G2P . . . EA 5 343.339 451.057 312.709 1 10.6 ? C6 G2P 501 B 1 HETATM 27 O O6 G2P . . . EA 5 342.818 449.931 312.673 1 10.55 ? O6 G2P 501 B 1 HETATM 28 N N1 G2P . . . EA 5 344.158 451.396 313.706 1 10.67 ? N1 G2P 501 B 1 HETATM 29 C C2 G2P . . . EA 5 344.744 452.61 313.776 1 10.69 ? C2 G2P 501 B 1 HETATM 30 N N2 G2P . . . EA 5 345.562 452.89 314.823 1 10.71 ? N2 G2P 501 B 1 HETATM 31 N N3 G2P . . . EA 5 344.555 453.568 312.831 1 10.66 ? N3 G2P 501 B 1 HETATM 32 C C4 G2P . . . EA 5 343.757 453.345 311.762 1 10.62 ? C4 G2P 501 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 61 _model_server_stats.query_time_ms 441 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #