data_6E7B # _model_server_result.job_id WgT7qm-sDx1GS991bV_d5Q _model_server_result.datetime_utc '2024-11-05 00:06:34' _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 6e7b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 6E7B # _exptl.entry_id 6E7B _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 521.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _entity.pdbx_number_of_molecules 1 _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 6E7B _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6E7B _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 A OG1 THR 143 B THR 143 1_555 C MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc2 C MG MG . B MG 501 1_555 D O1B G2P . B G2P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc3 C MG MG . B MG 501 1_555 D O1G G2P . B G2P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc4 C MG MG . B MG 501 1_555 D O3G G2P . B G2P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc5 C MG MG . B MG 501 1_555 D O3B G2P . B G2P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc6 C MG MG . B MG 501 1_555 D O2B G2P . B G2P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? metalc ? metalc7 B OE1 GLU 71 A GLU 71 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc8 E MG MG . A MG 501 1_555 F O2B GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc9 E MG MG . A MG 501 1_555 F O3G GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc10 E MG MG . A MG 501 1_555 F O3B GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.968 ? metalc ? metalc11 E MG MG . A MG 501 1_555 F O1B GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? # _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 6E7B _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 C 3 MG B 1 501 503 MG MG . D 4 G2P B 1 502 2 G2P G2P . E 3 MG A 1 501 502 MG MG . F 5 GTP A 1 502 1 GTP GTP . # 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 . . . D 4 103.767 39.746 -7.577 1 56.02 ? PG G2P 502 B 1 HETATM 2 O O1G G2P . . . D 4 102.65 40.39 -8.36 1 56.02 ? O1G G2P 502 B 1 HETATM 3 O O2G G2P . . . D 4 104.688 38.866 -8.386 1 56.02 ? O2G G2P 502 B 1 HETATM 4 O O3G G2P . . . D 4 104.457 40.709 -6.649 1 56.02 ? O3G G2P 502 B 1 HETATM 5 O O3B G2P . . . D 4 103.059 38.705 -6.579 1 56.02 ? O3B G2P 502 B 1 HETATM 6 P PB G2P . . . D 4 101.631 38.034 -6.894 1 56.02 ? PB G2P 502 B 1 HETATM 7 O O1B G2P . . . D 4 100.485 38.711 -5.99 1 56.02 ? O1B G2P 502 B 1 HETATM 8 O O2B G2P . . . D 4 101.271 38.177 -8.32 1 56.02 ? O2B G2P 502 B 1 HETATM 9 C C3A G2P . . . D 4 101.791 36.281 -6.473 1 56.02 ? C3A G2P 502 B 1 HETATM 10 P PA G2P . . . D 4 102.476 36.165 -4.807 1 56.02 ? PA G2P 502 B 1 HETATM 11 O O1A G2P . . . D 4 101.384 36.043 -3.818 1 56.02 ? O1A G2P 502 B 1 HETATM 12 O O2A G2P . . . D 4 103.301 37.517 -4.529 1 56.02 ? O2A G2P 502 B 1 HETATM 13 O O5' G2P . . . D 4 103.453 34.891 -4.705 1 56.02 ? O5' G2P 502 B 1 HETATM 14 C C5' G2P . . . D 4 104.062 34.586 -3.454 1 56.02 ? C5' G2P 502 B 1 HETATM 15 C C4' G2P . . . D 4 104.493 33.126 -3.259 1 56.02 ? C4' G2P 502 B 1 HETATM 16 O O4' G2P . . . D 4 103.679 32.58 -2.217 1 56.02 ? O4' G2P 502 B 1 HETATM 17 C C3' G2P . . . D 4 104.399 32.164 -4.445 1 56.02 ? C3' G2P 502 B 1 HETATM 18 O O3' G2P . . . D 4 105.699 31.664 -4.768 1 56.02 ? O3' G2P 502 B 1 HETATM 19 C C2' G2P . . . D 4 103.491 31.029 -4.017 1 56.02 ? C2' G2P 502 B 1 HETATM 20 O O2' G2P . . . D 4 104.156 29.775 -4.173 1 56.02 ? O2' G2P 502 B 1 HETATM 21 C C1' G2P . . . D 4 103.183 31.281 -2.547 1 56.02 ? C1' G2P 502 B 1 HETATM 22 N N9 G2P . . . D 4 101.738 31.21 -2.202 1 56.02 ? N9 G2P 502 B 1 HETATM 23 C C8 G2P . . . D 4 100.733 31.892 -2.782 1 56.02 ? C8 G2P 502 B 1 HETATM 24 N N7 G2P . . . D 4 99.543 31.586 -2.209 1 56.02 ? N7 G2P 502 B 1 HETATM 25 C C5 G2P . . . D 4 99.784 30.7 -1.233 1 56.02 ? C5 G2P 502 B 1 HETATM 26 C C6 G2P . . . D 4 98.975 29.97 -0.238 1 56.02 ? C6 G2P 502 B 1 HETATM 27 O O6 G2P . . . D 4 97.74 30.129 -0.185 1 56.02 ? O6 G2P 502 B 1 HETATM 28 N N1 G2P . . . D 4 99.6 29.139 0.601 1 56.02 ? N1 G2P 502 B 1 HETATM 29 C C2 G2P . . . D 4 100.933 28.954 0.559 1 56.02 ? C2 G2P 502 B 1 HETATM 30 N N2 G2P . . . D 4 101.509 28.096 1.435 1 56.02 ? N2 G2P 502 B 1 HETATM 31 N N3 G2P . . . D 4 101.737 29.59 -0.328 1 56.02 ? N3 G2P 502 B 1 HETATM 32 C C4 G2P . . . D 4 101.228 30.455 -1.232 1 56.02 ? C4 G2P 502 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #