data_5JCO # _model_server_result.job_id gU9BkSVewLfNNOcgctcX4w _model_server_result.datetime_utc '2025-02-27 17:10:23' _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 5jco # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"GA","auth_seq_id":501}' # _entry.id 5JCO # _exptl.entry_id 5JCO _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 521.208 _entity.id 3 _entity.src_method man _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 5JCO _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JCO _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 ? 3 M N N ? 3 Q N N ? 3 U N N ? 3 W N N ? 3 Y N N ? 3 GA 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 O2G G2P . K G2P 501 1_555 N MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc2 M O1B G2P . K G2P 501 1_555 N MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.968 ? metalc ? metalc3 O O3G GTP . H GTP 501 1_555 P MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc4 O O2B GTP . H GTP 501 1_555 P MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc5 Q O2G G2P . I G2P 501 1_555 R MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc6 S O3G GTP . E GTP 501 1_555 T MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc7 S O2B GTP . E GTP 501 1_555 T MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc8 U O2G G2P . J G2P 501 1_555 V MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc9 W O2G G2P . C G2P 501 1_555 X MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc10 Y O2G G2P . D G2P 501 1_555 Z MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc11 Y O1B G2P . D G2P 501 1_555 Z MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? metalc ? metalc12 AA O3G GTP . F GTP 501 1_555 BA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc13 AA O2B GTP . F GTP 501 1_555 BA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc14 CA O3G GTP . A GTP 501 1_555 DA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc15 CA O2B GTP . A GTP 501 1_555 DA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc16 EA O3G GTP . B GTP 501 1_555 FA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc17 EA O2B GTP . B GTP 501 1_555 FA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? metalc ? metalc18 GA O2G G2P . L G2P 501 1_555 HA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc19 GA O1B G2P . L G2P 501 1_555 HA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? metalc ? metalc20 IA O3G GTP . G GTP 501 1_555 JA MG MG . G MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc21 IA O2B GTP . G GTP 501 1_555 JA MG MG . G MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? # _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 5JCO _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 G2P K 1 501 501 G2P G2P . N 4 MG K 1 502 502 MG MG . O 5 GTP H 1 501 501 GTP GTP . P 4 MG H 1 502 502 MG MG . Q 3 G2P I 1 501 501 G2P G2P . R 4 MG I 1 502 502 MG MG . S 5 GTP E 1 501 501 GTP GTP . T 4 MG E 1 502 502 MG MG . U 3 G2P J 1 501 501 G2P G2P . V 4 MG J 1 502 502 MG MG . W 3 G2P C 1 501 501 G2P G2P . X 4 MG C 1 502 502 MG MG . Y 3 G2P D 1 501 501 G2P G2P . Z 4 MG D 1 502 502 MG MG . AA 5 GTP F 1 501 501 GTP GTP . BA 4 MG F 1 502 502 MG MG . CA 5 GTP A 1 501 501 GTP GTP . DA 4 MG A 1 502 502 MG MG . EA 5 GTP B 1 501 501 GTP GTP . FA 4 MG B 1 502 502 MG MG . GA 3 G2P L 1 501 501 G2P G2P . HA 4 MG L 1 502 502 MG MG . IA 5 GTP G 1 501 501 GTP GTP . JA 4 MG G 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 . . . GA 3 160.082 45.213 132.572 1 85.59 ? PG G2P 501 L 1 HETATM 2 O O1G G2P . . . GA 3 158.9 45.982 133.104 1 82.64 ? O1G G2P 501 L 1 HETATM 3 O O2G G2P . . . GA 3 159.886 43.716 132.584 1 88 ? O2G G2P 501 L 1 HETATM 4 O O3G G2P . . . GA 3 161.393 45.668 133.161 1 84.97 ? O3G G2P 501 L 1 HETATM 5 O O3B G2P . . . GA 3 160.197 45.585 131.01 1 79.79 ? O3B G2P 501 L 1 HETATM 6 P PB G2P . . . GA 3 159.139 44.974 129.969 1 75.55 ? PB G2P 501 L 1 HETATM 7 O O1B G2P . . . GA 3 159.395 43.537 129.729 1 74.07 ? O1B G2P 501 L 1 HETATM 8 O O2B G2P . . . GA 3 159.256 45.761 128.572 1 75.5 ? O2B G2P 501 L 1 HETATM 9 C C3A G2P . . . GA 3 157.489 45.167 130.688 1 76.56 ? C3A G2P 501 L 1 HETATM 10 P PA G2P . . . GA 3 156.283 44.562 129.502 1 78.95 ? PA G2P 501 L 1 HETATM 11 O O1A G2P . . . GA 3 155.201 43.864 130.23 1 79.4 ? O1A G2P 501 L 1 HETATM 12 O O2A G2P . . . GA 3 156.988 43.553 128.459 1 76.07 ? O2A G2P 501 L 1 HETATM 13 O O5' G2P . . . GA 3 155.72 45.856 128.719 1 75.48 ? O5' G2P 501 L 1 HETATM 14 C C5' G2P . . . GA 3 155.178 46.991 129.398 1 70.04 ? C5' G2P 501 L 1 HETATM 15 C C4' G2P . . . GA 3 153.859 47.413 128.739 1 68.46 ? C4' G2P 501 L 1 HETATM 16 O O4' G2P . . . GA 3 153.385 46.524 127.704 1 66.64 ? O4' G2P 501 L 1 HETATM 17 C C3' G2P . . . GA 3 152.719 47.503 129.736 1 66.08 ? C3' G2P 501 L 1 HETATM 18 O O3' G2P . . . GA 3 152.73 48.797 130.348 1 65.4 ? O3' G2P 501 L 1 HETATM 19 C C2' G2P . . . GA 3 151.469 47.202 128.912 1 65.49 ? C2' G2P 501 L 1 HETATM 20 O O2' G2P . . . GA 3 150.818 48.414 128.507 1 65.13 ? O2' G2P 501 L 1 HETATM 21 C C1' G2P . . . GA 3 151.945 46.441 127.679 1 64.15 ? C1' G2P 501 L 1 HETATM 22 N N9 G2P . . . GA 3 151.532 45.003 127.63 1 60.71 ? N9 G2P 501 L 1 HETATM 23 C C8 G2P . . . GA 3 151.688 44.083 128.6 1 58.65 ? C8 G2P 501 L 1 HETATM 24 N N7 G2P . . . GA 3 151.226 42.868 128.204 1 57.93 ? N7 G2P 501 L 1 HETATM 25 C C5 G2P . . . GA 3 150.761 42.972 126.946 1 59.07 ? C5 G2P 501 L 1 HETATM 26 C C6 G2P . . . GA 3 150.14 42.065 125.913 1 58.45 ? C6 G2P 501 L 1 HETATM 27 O O6 G2P . . . GA 3 149.897 40.849 126.094 1 54.55 ? O6 G2P 501 L 1 HETATM 28 N N1 G2P . . . GA 3 149.803 42.609 124.737 1 60.43 ? N1 G2P 501 L 1 HETATM 29 C C2 G2P . . . GA 3 150.024 43.921 124.463 1 63.59 ? C2 G2P 501 L 1 HETATM 30 N N2 G2P . . . GA 3 149.667 44.402 123.246 1 65.2 ? N2 G2P 501 L 1 HETATM 31 N N3 G2P . . . GA 3 150.594 44.794 125.348 1 61.8 ? N3 G2P 501 L 1 HETATM 32 C C4 G2P . . . GA 3 150.973 44.391 126.583 1 59.89 ? C4 G2P 501 L 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 70 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 32 #