data_5N5N # _model_server_result.job_id GEUNVdpxpNz5Mz2OEEA5nA _model_server_result.datetime_utc '2025-02-27 17:21:35' _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":"CA","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 . . . CA 3 59.915 48.931 200.06 1 54.59 ? PG G2P 501 C 1 HETATM 2 O O1G G2P . . . CA 3 59.08 47.675 200.133 1 54.5 ? O1G G2P 501 C 1 HETATM 3 O O2G G2P . . . CA 3 61.368 48.689 199.731 1 54.53 ? O2G G2P 501 C 1 HETATM 4 O O3G G2P . . . CA 3 59.696 49.891 201.206 1 54.61 ? O3G G2P 501 C 1 HETATM 5 O O3B G2P . . . CA 3 59.345 49.732 198.781 1 54.82 ? O3B G2P 501 C 1 HETATM 6 P PB G2P . . . CA 3 59.075 49.008 197.366 1 55.13 ? PB G2P 501 C 1 HETATM 7 O O1B G2P . . . CA 3 60.121 47.988 197.123 1 55.09 ? O1B G2P 501 C 1 HETATM 8 O O2B G2P . . . CA 3 59.131 50.111 196.195 1 54.99 ? O2B G2P 501 C 1 HETATM 9 C C3A G2P . . . CA 3 57.427 48.251 197.386 1 55.28 ? C3A G2P 501 C 1 HETATM 10 P PA G2P . . . CA 3 57.434 46.6 196.639 1 55.51 ? PA G2P 501 C 1 HETATM 11 O O1A G2P . . . CA 3 57.615 45.585 197.702 1 55.4 ? O1A G2P 501 C 1 HETATM 12 O O2A G2P . . . CA 3 58.625 46.48 195.562 1 55.56 ? O2A G2P 501 C 1 HETATM 13 O O5' G2P . . . CA 3 56.029 46.369 195.887 1 55.05 ? O5' G2P 501 C 1 HETATM 14 C C5' G2P . . . CA 3 54.857 45.993 196.608 1 54.47 ? C5' G2P 501 C 1 HETATM 15 C C4' G2P . . . CA 3 53.735 45.64 195.634 1 53.95 ? C4' G2P 501 C 1 HETATM 16 O O4' G2P . . . CA 3 54.224 44.762 194.617 1 53.18 ? O4' G2P 501 C 1 HETATM 17 C C3' G2P . . . CA 3 52.573 44.936 196.326 1 53.72 ? C3' G2P 501 C 1 HETATM 18 O O3' G2P . . . CA 3 51.348 45.641 196.083 1 53.85 ? O3' G2P 501 C 1 HETATM 19 C C2' G2P . . . CA 3 52.544 43.517 195.775 1 53.23 ? C2' G2P 501 C 1 HETATM 20 O O2' G2P . . . CA 3 51.248 43.152 195.284 1 53.51 ? O2' G2P 501 C 1 HETATM 21 C C1' G2P . . . CA 3 53.57 43.49 194.646 1 52.5 ? C1' G2P 501 C 1 HETATM 22 N N9 G2P . . . CA 3 54.596 42.428 194.821 1 51.33 ? N9 G2P 501 C 1 HETATM 23 C C8 G2P . . . CA 3 55.361 42.217 195.912 1 50.76 ? C8 G2P 501 C 1 HETATM 24 N N7 G2P . . . CA 3 56.197 41.165 195.717 1 50.62 ? N7 G2P 501 C 1 HETATM 25 C C5 G2P . . . CA 3 55.979 40.691 194.478 1 50.51 ? C5 G2P 501 C 1 HETATM 26 C C6 G2P . . . CA 3 56.52 39.598 193.629 1 50.35 ? C6 G2P 501 C 1 HETATM 27 O O6 G2P . . . CA 3 57.415 38.841 194.056 1 50.38 ? O6 G2P 501 C 1 HETATM 28 N N1 G2P . . . CA 3 56.02 39.438 192.391 1 50.38 ? N1 G2P 501 C 1 HETATM 29 C C2 G2P . . . CA 3 55.047 40.242 191.902 1 50.65 ? C2 G2P 501 C 1 HETATM 30 N N2 G2P . . . CA 3 54.584 40.032 190.645 1 50.8 ? N2 G2P 501 C 1 HETATM 31 N N3 G2P . . . CA 3 54.505 41.263 192.626 1 50.75 ? N3 G2P 501 C 1 HETATM 32 C C4 G2P . . . CA 3 54.923 41.53 193.891 1 50.81 ? C4 G2P 501 C 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #