data_3PIR # _model_server_result.job_id URhNbsTA54DuMrhMyqLAmA _model_server_result.datetime_utc '2024-11-13 22:08:13' _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 3pir # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":179}' # _entry.id 3PIR # _exptl.entry_id 3PIR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC 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 120 _cell.entry_id 3PIR _cell.length_a 109.421 _cell.length_b 109.421 _cell.length_c 68.211 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PIR _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 2 _struct_asym.id B _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 OG SER 32 A SER 27 1_555 C MG MG . A MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? metalc ? metalc2 B O2G GNP . A GNP 179 1_555 C MG MG . A MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc3 B O2B GNP . A GNP 179 1_555 C MG MG . A MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc4 C MG MG . A MG 180 1_555 D O HOH . A HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? metalc ? metalc5 C MG MG . A MG 180 1_555 D O HOH . A HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? # _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 116 n n PG O2G GNP sing 117 n n PG O3G GNP sing 118 n n PG N3B GNP sing 119 n n O2G HOG2 GNP sing 120 n n O3G HOG3 GNP sing 121 n n N3B PB GNP sing 122 n n N3B HNB3 GNP sing 123 n n PB O1B GNP doub 124 n n PB O2B GNP sing 125 n n PB O3A GNP sing 126 n n O2B HOB2 GNP sing 127 n n O3A PA GNP sing 128 n n PA O1A GNP doub 129 n n PA O2A GNP sing 130 n n PA O5' GNP sing 131 n n O2A HOA2 GNP sing 132 n n O5' C5' GNP sing 133 n n C5' C4' GNP sing 134 n n C5' "H5'2" GNP sing 135 n n C5' "H5'1" GNP sing 136 n n C4' O4' GNP sing 137 n n C4' C3' GNP sing 138 n n C4' H4' GNP sing 139 n n O4' C1' GNP sing 140 n n C3' O3' GNP sing 141 n n C3' C2' GNP sing 142 n n C3' H3' GNP sing 143 n n O3' HO3' GNP sing 144 n n C2' O2' GNP sing 145 n n C2' C1' GNP sing 146 n n C2' H2' GNP sing 147 n n O2' HO2' GNP sing 148 n n C1' N9 GNP sing 149 n n C1' H1' GNP sing 150 n n N9 C8 GNP sing 151 n y N9 C4 GNP sing 152 n y C8 N7 GNP doub 153 n y C8 H8 GNP sing 154 n n N7 C5 GNP sing 155 n y C5 C6 GNP sing 156 n y C5 C4 GNP doub 157 n y C6 O6 GNP doub 158 n n C6 N1 GNP sing 159 n y N1 C2 GNP sing 160 n y N1 HN1 GNP sing 161 n n C2 N2 GNP sing 162 n n C2 N3 GNP doub 163 n y N2 HN21 GNP sing 164 n n N2 HN22 GNP sing 165 n n N3 C4 GNP sing 166 n y # _atom_sites.entry_id 3PIR _atom_sites.fract_transf_matrix[1][1] 0.009139 _atom_sites.fract_transf_matrix[1][2] 0.005276 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010553 _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] 0.01466 _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 B 2 GNP A 1 179 179 GNP GNP . C 3 MG A 1 180 180 MG MG . D 4 HOH A 1 1001 1001 HOH HOH . D 4 HOH A 2 1002 1002 HOH HOH . D 4 HOH A 3 1003 1003 HOH HOH . D 4 HOH A 4 1004 1004 HOH HOH . D 4 HOH A 5 1005 1005 HOH HOH . D 4 HOH A 6 1006 1006 HOH HOH . D 4 HOH A 7 1007 1007 HOH HOH . D 4 HOH A 8 1008 1008 HOH HOH . D 4 HOH A 9 1009 1009 HOH HOH . D 4 HOH A 10 1010 1010 HOH HOH . D 4 HOH A 11 1011 1011 HOH HOH . D 4 HOH A 12 1012 1012 HOH HOH . D 4 HOH A 13 1013 1013 HOH HOH . D 4 HOH A 14 1014 1014 HOH HOH . D 4 HOH A 15 1015 1015 HOH HOH . D 4 HOH A 16 1016 1016 HOH HOH . D 4 HOH A 17 1017 1017 HOH HOH . D 4 HOH A 18 1018 1018 HOH HOH . D 4 HOH A 19 1019 1019 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 . . . B 2 -12.129 45.359 9.33 1 15.67 ? PG GNP 179 A 1 HETATM 2 O O1G GNP . . . B 2 -13.352 46.017 8.691 1 12.46 ? O1G GNP 179 A 1 HETATM 3 O O2G GNP . . . B 2 -11.172 44.803 8.302 1 16.03 ? O2G GNP 179 A 1 HETATM 4 O O3G GNP . . . B 2 -12.61 44.306 10.332 1 15.43 ? O3G GNP 179 A 1 HETATM 5 N N3B GNP . . . B 2 -11.287 46.448 10.164 1 14.6 ? N3B GNP 179 A 1 HETATM 6 P PB GNP . . . B 2 -9.687 46.414 10.343 1 14.87 ? PB GNP 179 A 1 HETATM 7 O O1B GNP . . . B 2 -9.404 45.882 11.709 1 15.7 ? O1B GNP 179 A 1 HETATM 8 O O2B GNP . . . B 2 -9.074 45.645 9.21 1 8.6 ? O2B GNP 179 A 1 HETATM 9 O O3A GNP . . . B 2 -9.204 47.874 10.414 1 11.7 ? O3A GNP 179 A 1 HETATM 10 P PA GNP . . . B 2 -8.315 48.573 9.375 1 11.16 ? PA GNP 179 A 1 HETATM 11 O O1A GNP . . . B 2 -8.959 48.391 8.051 1 11.46 ? O1A GNP 179 A 1 HETATM 12 O O2A GNP . . . B 2 -6.916 48.108 9.45 1 10.74 ? O2A GNP 179 A 1 HETATM 13 O O5' GNP . . . B 2 -8.246 50.117 9.724 1 9.21 ? O5' GNP 179 A 1 HETATM 14 C C5' GNP . . . B 2 -9.364 50.955 10.036 1 8.76 ? C5' GNP 179 A 1 HETATM 15 C C4' GNP . . . B 2 -8.874 52.403 9.931 1 11.91 ? C4' GNP 179 A 1 HETATM 16 O O4' GNP . . . B 2 -7.956 52.816 11.013 1 10.28 ? O4' GNP 179 A 1 HETATM 17 C C3' GNP . . . B 2 -8.081 52.646 8.646 1 12.76 ? C3' GNP 179 A 1 HETATM 18 O O3' GNP . . . B 2 -8.324 53.967 8.23 1 16.04 ? O3' GNP 179 A 1 HETATM 19 C C2' GNP . . . B 2 -6.625 52.519 9.061 1 12.7 ? C2' GNP 179 A 1 HETATM 20 O O2' GNP . . . B 2 -5.809 53.329 8.238 1 13.3 ? O2' GNP 179 A 1 HETATM 21 C C1' GNP . . . B 2 -6.657 53.076 10.491 1 11.85 ? C1' GNP 179 A 1 HETATM 22 N N9 GNP . . . B 2 -5.652 52.601 11.461 1 11.85 ? N9 GNP 179 A 1 HETATM 23 C C8 GNP . . . B 2 -5.362 51.297 11.785 1 11.89 ? C8 GNP 179 A 1 HETATM 24 N N7 GNP . . . B 2 -4.425 51.172 12.691 1 11.53 ? N7 GNP 179 A 1 HETATM 25 C C5 GNP . . . B 2 -4.074 52.473 13.006 1 12.16 ? C5 GNP 179 A 1 HETATM 26 C C6 GNP . . . B 2 -3.12 52.948 13.948 1 15.48 ? C6 GNP 179 A 1 HETATM 27 O O6 GNP . . . B 2 -2.388 52.274 14.685 1 18.62 ? O6 GNP 179 A 1 HETATM 28 N N1 GNP . . . B 2 -3.034 54.349 13.994 1 15.85 ? N1 GNP 179 A 1 HETATM 29 C C2 GNP . . . B 2 -3.799 55.201 13.185 1 14.55 ? C2 GNP 179 A 1 HETATM 30 N N2 GNP . . . B 2 -3.566 56.519 13.34 1 9.98 ? N2 GNP 179 A 1 HETATM 31 N N3 GNP . . . B 2 -4.707 54.759 12.29 1 11.78 ? N3 GNP 179 A 1 HETATM 32 C C4 GNP . . . B 2 -4.803 53.379 12.256 1 12.5 ? C4 GNP 179 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 32 #