data_5DHA # _model_server_result.job_id z0Vjof5zozy0ls5OQ60Oqw _model_server_result.datetime_utc '2024-11-26 08:52:36' _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 5dha # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 5DHA # _exptl.entry_id 5DHA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 5 _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 90 _cell.entry_id 5DHA _cell.length_a 106.279 _cell.length_b 106.279 _cell.length_c 304.57 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DHA _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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,K _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 5 _struct_asym.id E _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 45 A THR 24 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc2 A OG1 THR 63 A THR 42 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc3 E O2G GNP . A GNP 301 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? metalc ? metalc4 E O1B GNP . A GNP 301 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc5 F MG MG . A MG 302 1_555 J O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc6 F MG MG . A MG 302 1_555 J O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? # _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 5DHA _atom_sites.fract_transf_matrix[1][1] 0.009409 _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] 0.009409 _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] 0.003283 _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 5 GNP A 1 301 301 GNP GNP . F 6 MG A 1 302 302 MG MG . G 7 GOL A 1 303 1 GOL GOL . H 7 GOL C 1 1101 2 GOL GOL . I 7 GOL C 1 1102 3 GOL GOL . J 8 HOH A 1 401 1 HOH HOH . J 8 HOH A 2 402 2 HOH HOH . K 8 HOH C 1 1201 6 HOH HOH . K 8 HOH C 2 1202 3 HOH HOH . K 8 HOH C 3 1203 5 HOH HOH . K 8 HOH C 4 1204 4 HOH HOH . K 8 HOH C 5 1205 8 HOH HOH . K 8 HOH C 6 1206 7 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 . . . E 5 6.574 37.296 28.495 1 27.32 ? PG GNP 301 A 1 HETATM 2 O O1G GNP . . . E 5 6.815 35.965 27.819 1 29.25 ? O1G GNP 301 A 1 HETATM 3 O O2G GNP . . . E 5 7.829 38.13 28.404 1 28.58 ? O2G GNP 301 A 1 HETATM 4 O O3G GNP . . . E 5 6.226 37.058 29.945 1 26.45 ? O3G GNP 301 A 1 HETATM 5 N N3B GNP . . . E 5 5.336 38.093 27.743 1 49.13 ? N3B GNP 301 A 1 HETATM 6 P PB GNP . . . E 5 4.964 39.65 28.162 1 25.77 ? PB GNP 301 A 1 HETATM 7 O O1B GNP . . . E 5 6.23 40.45 28.345 1 27.77 ? O1B GNP 301 A 1 HETATM 8 O O2B GNP . . . E 5 4.202 39.651 29.464 1 25.2 ? O2B GNP 301 A 1 HETATM 9 O O3A GNP . . . E 5 4.068 40.318 27.043 1 25.94 ? O3A GNP 301 A 1 HETATM 10 P PA GNP . . . E 5 4.614 41.323 25.953 1 23.2 ? PA GNP 301 A 1 HETATM 11 O O1A GNP . . . E 5 5.804 40.705 25.258 1 24.01 ? O1A GNP 301 A 1 HETATM 12 O O2A GNP . . . E 5 5.026 42.622 26.603 1 23.67 ? O2A GNP 301 A 1 HETATM 13 O O5' GNP . . . E 5 3.48 41.599 24.889 1 35.37 ? O5' GNP 301 A 1 HETATM 14 C C5' GNP . . . E 5 2.978 40.483 24.193 1 37.7 ? C5' GNP 301 A 1 HETATM 15 C C4' GNP . . . E 5 1.863 40.925 23.23 1 37.47 ? C4' GNP 301 A 1 HETATM 16 O O4' GNP . . . E 5 0.945 41.562 23.899 1 40.57 ? O4' GNP 301 A 1 HETATM 17 C C3' GNP . . . E 5 2.429 41.913 22.203 1 34.73 ? C3' GNP 301 A 1 HETATM 18 O O3' GNP . . . E 5 2.207 41.456 20.945 1 30.11 ? O3' GNP 301 A 1 HETATM 19 C C2' GNP . . . E 5 1.678 43.238 22.451 1 36.33 ? C2' GNP 301 A 1 HETATM 20 O O2' GNP . . . E 5 1.375 43.893 21.141 1 36.76 ? O2' GNP 301 A 1 HETATM 21 C C1' GNP . . . E 5 0.583 42.893 23.064 1 36.61 ? C1' GNP 301 A 1 HETATM 22 N N9 GNP . . . E 5 0.103 43.878 23.968 1 34.56 ? N9 GNP 301 A 1 HETATM 23 C C8 GNP . . . E 5 0.735 44.297 25.092 1 33.77 ? C8 GNP 301 A 1 HETATM 24 N N7 GNP . . . E 5 -0.042 45.229 25.687 1 33 ? N7 GNP 301 A 1 HETATM 25 C C5 GNP . . . E 5 -1.165 45.382 24.937 1 32.3 ? C5 GNP 301 A 1 HETATM 26 C C6 GNP . . . E 5 -2.277 46.196 25.087 1 30.43 ? C6 GNP 301 A 1 HETATM 27 O O6 GNP . . . E 5 -2.356 46.944 26.042 1 26.59 ? O6 GNP 301 A 1 HETATM 28 N N1 GNP . . . E 5 -3.269 46.148 24.181 1 32.77 ? N1 GNP 301 A 1 HETATM 29 C C2 GNP . . . E 5 -3.178 45.3 23.111 1 33.68 ? C2 GNP 301 A 1 HETATM 30 N N2 GNP . . . E 5 -4.213 45.233 22.139 1 33.74 ? N2 GNP 301 A 1 HETATM 31 N N3 GNP . . . E 5 -2.082 44.501 22.963 1 32.93 ? N3 GNP 301 A 1 HETATM 32 C C4 GNP . . . E 5 -1.077 44.546 23.881 1 32.89 ? C4 GNP 301 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #