data_5N5N # _model_server_result.job_id p3wgD0YRtcayK2rCa-Fa-w _model_server_result.datetime_utc '2025-07-07 19:23:57' _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 5n5n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"AA","auth_seq_id":501}' # _entry.id 5N5N # _exptl.entry_id 5N5N _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 521.208 _entity.id 3 _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 5N5N _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5N5N _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 PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,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 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 M N N ? 3 AA N N ? 3 CA N N ? 3 EA N N ? 3 GA N N ? 3 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 O2G G2P . B G2P 501 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc2 O O1G GTP . K GTP 501 1_555 P MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc3 O O3G GTP . K GTP 501 1_555 P MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc4 Q O1G GTP . G GTP 501 1_555 R MG MG . G MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc5 Q O3G GTP . G GTP 501 1_555 R MG MG . G MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? metalc ? metalc6 S O1G GTP . H GTP 501 1_555 T MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc7 S O3G GTP . H GTP 501 1_555 T MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc8 U O1G GTP . I GTP 501 1_555 V MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc9 U O3G GTP . I GTP 501 1_555 V MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc10 U O2B GTP . I GTP 501 1_555 V MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? metalc ? metalc11 W O1G GTP . J GTP 501 1_555 X MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc12 W O3G GTP . J GTP 501 1_555 X MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc13 W O2B GTP . J GTP 501 1_555 X MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc14 Y O1G GTP . L GTP 501 1_555 Z MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc15 Y O3G GTP . L GTP 501 1_555 Z MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc16 Y O3B GTP . L GTP 501 1_555 Z MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc17 Y O2B GTP . L GTP 501 1_555 Z MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc18 AA O2G G2P . A G2P 501 1_555 BA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc19 CA O2G G2P . C G2P 501 1_555 DA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc20 EA O2G G2P . D G2P 501 1_555 FA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc21 GA O2G G2P . E G2P 501 1_555 HA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc22 IA O2G G2P . F G2P 501 1_555 JA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? # _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 5N5N _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 B 1 501 501 G2P G2P . N 4 MG B 1 502 502 MG MG . O 5 GTP K 1 501 501 GTP GTP . P 4 MG K 1 502 502 MG MG . Q 5 GTP G 1 501 501 GTP GTP . R 4 MG G 1 502 502 MG MG . S 5 GTP H 1 501 501 GTP GTP . T 4 MG H 1 502 502 MG MG . U 5 GTP I 1 501 501 GTP GTP . V 4 MG I 1 502 502 MG MG . W 5 GTP J 1 501 501 GTP GTP . X 4 MG J 1 502 502 MG MG . Y 5 GTP L 1 501 501 GTP GTP . Z 4 MG L 1 502 502 MG MG . AA 3 G2P A 1 501 501 G2P G2P . BA 4 MG A 1 502 502 MG MG . CA 3 G2P C 1 501 501 G2P G2P . DA 4 MG C 1 502 502 MG MG . EA 3 G2P D 1 501 501 G2P G2P . FA 4 MG D 1 502 502 MG MG . GA 3 G2P E 1 501 501 G2P G2P . HA 4 MG E 1 502 502 MG MG . IA 3 G2P F 1 501 501 G2P G2P . JA 4 MG F 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 . . . AA 3 112.326 58.644 209.015 1 57.58 ? PG G2P 501 A 1 HETATM 2 O O1G G2P . . . AA 3 111.032 57.866 209.061 1 57.47 ? O1G G2P 501 A 1 HETATM 3 O O2G G2P . . . AA 3 113.538 57.81 208.681 1 57.53 ? O2G G2P 501 A 1 HETATM 4 O O3G G2P . . . AA 3 112.528 59.582 210.181 1 57.63 ? O3G G2P 501 A 1 HETATM 5 O O3B G2P . . . AA 3 112.165 59.636 207.753 1 57.91 ? O3B G2P 501 A 1 HETATM 6 P PB G2P . . . AA 3 111.615 59.126 206.326 1 58.31 ? PB G2P 501 A 1 HETATM 7 O O1B G2P . . . AA 3 112.127 57.763 206.058 1 58.29 ? O1B G2P 501 A 1 HETATM 8 O O2B G2P . . . AA 3 112.142 60.122 205.176 1 58.09 ? O2B G2P 501 A 1 HETATM 9 C C3A G2P . . . AA 3 109.801 59.145 206.344 1 58.61 ? C3A G2P 501 A 1 HETATM 10 P PA G2P . . . AA 3 109.1 57.64 205.618 1 58.98 ? PA G2P 501 A 1 HETATM 11 O O1A G2P . . . AA 3 108.846 56.655 206.694 1 58.84 ? O1A G2P 501 A 1 HETATM 12 O O2A G2P . . . AA 3 110.117 57.018 204.535 1 59.06 ? O2A G2P 501 A 1 HETATM 13 O O5' G2P . . . AA 3 107.722 58.017 204.876 1 58.74 ? O5' G2P 501 A 1 HETATM 14 C C5' G2P . . . AA 3 106.503 58.151 205.605 1 58.39 ? C5' G2P 501 A 1 HETATM 15 C C4' G2P . . . AA 3 105.334 58.334 204.641 1 58.02 ? C4' G2P 501 A 1 HETATM 16 O O4' G2P . . . AA 3 105.398 57.354 203.601 1 57.34 ? O4' G2P 501 A 1 HETATM 17 C C3' G2P . . . AA 3 103.987 58.175 205.336 1 57.9 ? C3' G2P 501 A 1 HETATM 18 O O3' G2P . . . AA 3 103.173 59.336 205.116 1 58.04 ? O3' G2P 501 A 1 HETATM 19 C C2' G2P . . . AA 3 103.358 56.911 204.769 1 57.46 ? C2' G2P 501 A 1 HETATM 20 O O2' G2P . . . AA 3 102.02 57.131 204.304 1 57.79 ? O2' G2P 501 A 1 HETATM 21 C C1' G2P . . . AA 3 104.263 56.483 203.618 1 56.75 ? C1' G2P 501 A 1 HETATM 22 N N9 G2P . . . AA 3 104.735 55.08 203.749 1 55.63 ? N9 G2P 501 A 1 HETATM 23 C C8 G2P . . . AA 3 105.356 54.533 204.814 1 55.09 ? C8 G2P 501 A 1 HETATM 24 N N7 G2P . . . AA 3 105.654 53.229 204.579 1 55.01 ? N7 G2P 501 A 1 HETATM 25 C C5 G2P . . . AA 3 105.228 52.927 203.34 1 54.92 ? C5 G2P 501 A 1 HETATM 26 C C6 G2P . . . AA 3 105.228 51.73 202.459 1 54.8 ? C6 G2P 501 A 1 HETATM 27 O O6 G2P . . . AA 3 105.719 50.651 202.848 1 54.79 ? O6 G2P 501 A 1 HETATM 28 N N1 G2P . . . AA 3 104.682 51.835 201.234 1 54.89 ? N1 G2P 501 A 1 HETATM 29 C C2 G2P . . . AA 3 104.141 52.993 200.786 1 55.18 ? C2 G2P 501 A 1 HETATM 30 N N2 G2P . . . AA 3 103.607 53.036 199.54 1 55.38 ? N2 G2P 501 A 1 HETATM 31 N N3 G2P . . . AA 3 104.107 54.127 201.541 1 55.21 ? N3 G2P 501 A 1 HETATM 32 C C4 G2P . . . AA 3 104.624 54.154 202.797 1 55.19 ? C4 G2P 501 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 32 #