data_8V4K # _model_server_result.job_id sAQGkW_-Kcm9yjSIuPWkrw _model_server_result.datetime_utc '2024-11-09 02:40:09' _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 8v4k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":502}' # _entry.id 8V4K # _exptl.entry_id 8V4K _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 8V4K _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8V4K _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 ? 6 I N N ? 6 O 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 B CD GLU 435 B GLU 435 1_555 K N GLU . B GLU 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? metalc ? metalc1 F MG MG . A MG 501 1_555 G O3G GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc2 F MG MG . A MG 501 1_555 G O2B GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc3 B OE2 GLU 69 B GLU 69 1_555 H MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc4 B OE1 GLU 435 B GLU 435 1_555 J ZN ZN . B ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.719 ? metalc ? metalc5 H MG MG . B MG 501 1_555 I O2G G2P . B G2P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc6 J ZN ZN . B ZN 503 1_555 E ND1 HIS 252 E HIS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc7 J ZN ZN . B ZN 503 1_555 E OE1 GLU 255 E GLU 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc8 J ZN ZN . B ZN 503 1_555 E OE2 GLU 255 E GLU 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc9 J ZN ZN . B ZN 503 1_555 E ND1 HIS 434 E HIS 434 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc10 C OE2 GLU 71 C GLU 71 1_555 L MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc11 L MG MG . C MG 501 1_555 M O2B GTP . C GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc12 L MG MG . C MG 501 1_555 M O2G GTP . C GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc13 L MG MG . C MG 501 1_555 M O3G GTP . C GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc14 N MG MG . D MG 501 1_555 O O2G G2P . D G2P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? # _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 8V4K _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 F 4 MG A 1 501 502 MG MG . G 5 GTP A 1 502 503 GTP GTP . H 4 MG B 1 501 502 MG MG . I 6 G2P B 1 502 503 G2P G2P . J 7 ZN B 1 503 701 ZN ZN . K 8 GLU B 1 1001 435 GLU GLX . L 4 MG C 1 501 502 MG MG . M 5 GTP C 1 502 503 GTP GTP . N 4 MG D 1 501 502 MG MG . O 6 G2P D 1 502 503 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 . . . O 6 347.419 392.855 318.814 1 117.42 ? PG G2P 502 D 1 HETATM 2 O O1G G2P . . . O 6 346.981 393.446 320.131 1 116.18 ? O1G G2P 502 D 1 HETATM 3 O O2G G2P . . . O 6 347.453 391.347 318.831 1 109.12 ? O2G G2P 502 D 1 HETATM 4 O O3G G2P . . . O 6 348.697 393.459 318.303 1 111.39 ? O3G G2P 502 D 1 HETATM 5 O O3B G2P . . . O 6 346.282 393.249 317.745 1 114.26 ? O3B G2P 502 D 1 HETATM 6 P PB G2P . . . O 6 346.16 392.987 316.184 1 112.16 ? PB G2P 502 D 1 HETATM 7 O O1B G2P . . . O 6 347.241 393.734 315.454 1 112.41 ? O1B G2P 502 D 1 HETATM 8 O O2B G2P . . . O 6 346.097 391.506 315.941 1 104.48 ? O2B G2P 502 D 1 HETATM 9 C C3A G2P . . . O 6 344.56 393.704 315.707 1 107.12 ? C3A G2P 502 D 1 HETATM 10 P PA G2P . . . O 6 343.171 392.546 315.855 1 108.52 ? PA G2P 502 D 1 HETATM 11 O O1A G2P . . . O 6 343.242 391.612 314.681 1 106.62 ? O1A G2P 502 D 1 HETATM 12 O O2A G2P . . . O 6 343.248 391.906 317.212 1 110.69 ? O2A G2P 502 D 1 HETATM 13 O O5' G2P . . . O 6 341.861 393.438 315.765 1 105.7 ? O5' G2P 502 D 1 HETATM 14 C C5' G2P . . . O 6 341.841 394.708 315.067 1 104.17 ? C5' G2P 502 D 1 HETATM 15 C C4' G2P . . . O 6 340.418 395.09 314.741 1 106.4 ? C4' G2P 502 D 1 HETATM 16 O O4' G2P . . . O 6 339.844 394.068 313.885 1 104.59 ? O4' G2P 502 D 1 HETATM 17 C C3' G2P . . . O 6 339.455 395.222 315.931 1 110.63 ? C3' G2P 502 D 1 HETATM 18 O O3' G2P . . . O 6 338.551 396.299 315.727 1 111.83 ? O3' G2P 502 D 1 HETATM 19 C C2' G2P . . . O 6 338.713 393.884 315.908 1 110.17 ? C2' G2P 502 D 1 HETATM 20 O O2' G2P . . . O 6 337.45 393.93 316.537 1 119.78 ? O2' G2P 502 D 1 HETATM 21 C C1' G2P . . . O 6 338.603 393.658 314.406 1 104.63 ? C1' G2P 502 D 1 HETATM 22 N N9 G2P . . . O 6 338.397 392.264 314.039 1 103.39 ? N9 G2P 502 D 1 HETATM 23 C C8 G2P . . . O 6 338.773 391.162 314.762 1 103.45 ? C8 G2P 502 D 1 HETATM 24 N N7 G2P . . . O 6 338.459 390.03 314.18 1 104.46 ? N7 G2P 502 D 1 HETATM 25 C C5 G2P . . . O 6 337.839 390.415 312.999 1 102.97 ? C5 G2P 502 D 1 HETATM 26 C C6 G2P . . . O 6 337.288 389.624 311.962 1 101.01 ? C6 G2P 502 D 1 HETATM 27 O O6 G2P . . . O 6 337.237 388.389 311.884 1 100.86 ? O6 G2P 502 D 1 HETATM 28 N N1 G2P . . . O 6 336.756 390.417 310.946 1 99.19 ? N1 G2P 502 D 1 HETATM 29 C C2 G2P . . . O 6 336.756 391.79 310.927 1 101.98 ? C2 G2P 502 D 1 HETATM 30 N N2 G2P . . . O 6 336.197 392.376 309.86 1 104.02 ? N2 G2P 502 D 1 HETATM 31 N N3 G2P . . . O 6 337.274 392.539 311.899 1 104.31 ? N3 G2P 502 D 1 HETATM 32 C C4 G2P . . . O 6 337.794 391.788 312.899 1 104.27 ? C4 G2P 502 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 183 _model_server_stats.query_time_ms 369 _model_server_stats.encode_time_ms 54 _model_server_stats.element_count 32 #