data_4DCN # _model_server_result.job_id 3cr0G-IFu-MW-fyn-fu88g _model_server_result.datetime_utc '2024-10-11 06:23:40' _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 4dcn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":202}' # _entry.id 4DCN # _exptl.entry_id 4DCN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC 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 4DCN _cell.length_a 62.764 _cell.length_b 111.125 _cell.length_c 119.809 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DCN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 4 F N N ? 4 H 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 A OG1 THR 18 A THR 31 1_555 E MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc2 A OG1 THR 35 A THR 48 1_555 E MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc3 E MG MG . A MG 201 1_555 F O2G GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? metalc ? metalc4 E MG MG . A MG 201 1_555 F O2B GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc5 E MG MG . A MG 201 1_555 I O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? metalc ? metalc6 E MG MG . A MG 201 1_555 I O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc7 B OG1 THR 18 B THR 31 1_555 G MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc8 B OG1 THR 35 B THR 48 1_555 G MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc9 G MG MG . B MG 201 1_555 H O2B GNP . B GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.871 ? metalc ? metalc10 G MG MG . B MG 201 1_555 H O2G GNP . B GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.666 ? metalc ? metalc11 G MG MG . B MG 201 1_555 J O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc12 G MG MG . B MG 201 1_555 J O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC 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 GNP doub 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 4DCN _atom_sites.fract_transf_matrix[1][1] 0.015933 _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] 0.008999 _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] 0.008347 _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 E 3 MG A 1 201 1 MG MG . F 4 GNP A 1 202 1 GNP GNP . G 3 MG B 1 201 1 MG MG . H 4 GNP B 1 202 1 GNP GNP . I 5 HOH A 1 301 3 HOH HOH . I 5 HOH A 2 302 4 HOH HOH . J 5 HOH B 1 301 1 HOH HOH . J 5 HOH B 2 302 2 HOH HOH . # 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 GNP . . . F 4 -22.7 51.609 -10.829 1 61.33 ? PG GNP 202 A 1 HETATM 2 O O1G GNP . . . F 4 -22.636 52.586 -11.971 1 60.82 ? O1G GNP 202 A 1 HETATM 3 O O2G GNP . . . F 4 -21.745 50.445 -10.91 1 61.42 ? O2G GNP 202 A 1 HETATM 4 O O3G GNP . . . F 4 -22.534 52.466 -9.6 1 61.33 ? O3G GNP 202 A 1 HETATM 5 N N3B GNP . . . F 4 -24.168 51.013 -10.73 1 62.45 ? N3B GNP 202 A 1 HETATM 6 P PB GNP . . . F 4 -24.837 50.105 -11.849 1 63.68 ? PB GNP 202 A 1 HETATM 7 O O1B GNP . . . F 4 -25.241 50.926 -13.013 1 63.3 ? O1B GNP 202 A 1 HETATM 8 O O2B GNP . . . F 4 -23.883 49 -12.088 1 64.03 ? O2B GNP 202 A 1 HETATM 9 O O3A GNP . . . F 4 -26.135 49.516 -11.279 1 65.03 ? O3A GNP 202 A 1 HETATM 10 P PA GNP . . . F 4 -26.372 48.032 -10.976 1 66.12 ? PA GNP 202 A 1 HETATM 11 O O1A GNP . . . F 4 -26.444 47.298 -12.255 1 66.09 ? O1A GNP 202 A 1 HETATM 12 O O2A GNP . . . F 4 -25.398 47.535 -9.98 1 66.04 ? O2A GNP 202 A 1 HETATM 13 O O5' GNP . . . F 4 -27.802 47.907 -10.311 1 67.11 ? O5' GNP 202 A 1 HETATM 14 C C5' GNP . . . F 4 -28.003 48.333 -8.965 1 68.94 ? C5' GNP 202 A 1 HETATM 15 C C4' GNP . . . F 4 -29.38 47.955 -8.447 1 70.47 ? C4' GNP 202 A 1 HETATM 16 O O4' GNP . . . F 4 -30.398 48.674 -9.188 1 70.98 ? O4' GNP 202 A 1 HETATM 17 C C3' GNP . . . F 4 -29.773 46.488 -8.589 1 71.35 ? C3' GNP 202 A 1 HETATM 18 O O3' GNP . . . F 4 -29.25 45.711 -7.52 1 71.85 ? O3' GNP 202 A 1 HETATM 19 C C2' GNP . . . F 4 -31.295 46.577 -8.521 1 71.8 ? C2' GNP 202 A 1 HETATM 20 O O2' GNP . . . F 4 -31.787 46.69 -7.195 1 72.06 ? O2' GNP 202 A 1 HETATM 21 C C1' GNP . . . F 4 -31.559 47.865 -9.302 1 71.72 ? C1' GNP 202 A 1 HETATM 22 N N9 GNP . . . F 4 -31.879 47.645 -10.717 1 72.08 ? N9 GNP 202 A 1 HETATM 23 C C8 GNP . . . F 4 -30.999 47.507 -11.767 1 72.16 ? C8 GNP 202 A 1 HETATM 24 N N7 GNP . . . F 4 -31.579 47.324 -12.921 1 72.12 ? N7 GNP 202 A 1 HETATM 25 C C5 GNP . . . F 4 -32.934 47.339 -12.622 1 72.29 ? C5 GNP 202 A 1 HETATM 26 C C6 GNP . . . F 4 -34.058 47.186 -13.468 1 72.45 ? C6 GNP 202 A 1 HETATM 27 O O6 GNP . . . F 4 -34.071 47.008 -14.69 1 73.07 ? O6 GNP 202 A 1 HETATM 28 N N1 GNP . . . F 4 -35.264 47.263 -12.77 1 72.51 ? N1 GNP 202 A 1 HETATM 29 C C2 GNP . . . F 4 -35.369 47.463 -11.413 1 72.41 ? C2 GNP 202 A 1 HETATM 30 N N2 GNP . . . F 4 -36.61 47.511 -10.908 1 72.43 ? N2 GNP 202 A 1 HETATM 31 N N3 GNP . . . F 4 -34.322 47.606 -10.606 1 72.39 ? N3 GNP 202 A 1 HETATM 32 C C4 GNP . . . F 4 -33.138 47.533 -11.272 1 72.27 ? C4 GNP 202 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #