data_3TNF # _model_server_result.job_id eWHjK7uPg4q91eZXgnSOfA _model_server_result.datetime_utc '2024-11-25 18:53:55' _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 3tnf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":200}' # _entry.id 3TNF # _exptl.entry_id 3TNF _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 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 3TNF _cell.length_a 103.82 _cell.length_b 103.82 _cell.length_c 150.61 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TNF _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _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 20 A THR 22 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc2 A OG1 THR 38 A THR 40 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc3 A O THR 62 A THR 64 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc4 C MG MG . A MG 199 1_555 D O2B GNP . A GNP 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc5 C MG MG . A MG 199 1_555 D O2G GNP . A GNP 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? # _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 3TNF _atom_sites.fract_transf_matrix[1][1] 0.009632 _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] 0.009632 _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] 0.00664 _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 A 1 199 199 MG MG . D 4 GNP A 1 200 200 GNP GNP . E 5 MPD A 1 1 1 MPD MPD . F 5 MPD A 1 177 4 MPD MPD . G 5 MPD B 1 2 2 MPD MPD . H 5 MPD B 1 3 3 MPD MPD . I 6 HOH A 1 2 2 HOH HOH . I 6 HOH A 2 178 1 HOH HOH . I 6 HOH A 3 179 3 HOH HOH . I 6 HOH A 4 180 4 HOH HOH . I 6 HOH A 5 181 5 HOH HOH . I 6 HOH A 6 182 6 HOH HOH . I 6 HOH A 7 183 7 HOH HOH . I 6 HOH A 8 184 8 HOH HOH . I 6 HOH A 9 185 9 HOH HOH . I 6 HOH A 10 186 10 HOH HOH . I 6 HOH A 11 187 11 HOH HOH . I 6 HOH A 12 188 12 HOH HOH . I 6 HOH A 13 189 13 HOH HOH . I 6 HOH A 14 190 14 HOH HOH . I 6 HOH A 15 191 15 HOH HOH . I 6 HOH A 16 192 16 HOH HOH . I 6 HOH A 17 193 17 HOH HOH . I 6 HOH A 18 194 18 HOH HOH . I 6 HOH A 19 195 19 HOH HOH . I 6 HOH A 20 196 20 HOH HOH . I 6 HOH A 21 197 21 HOH HOH . I 6 HOH A 22 198 22 HOH HOH . I 6 HOH A 23 201 23 HOH HOH . I 6 HOH A 24 202 24 HOH HOH . I 6 HOH A 25 203 25 HOH HOH . I 6 HOH A 26 204 26 HOH HOH . J 6 HOH B 1 27 27 HOH HOH . J 6 HOH B 2 28 28 HOH HOH . J 6 HOH B 3 29 29 HOH HOH . J 6 HOH B 4 30 30 HOH HOH . J 6 HOH B 5 31 31 HOH HOH . J 6 HOH B 6 32 32 HOH HOH . J 6 HOH B 7 33 33 HOH HOH . J 6 HOH B 8 34 34 HOH HOH . J 6 HOH B 9 35 35 HOH HOH . J 6 HOH B 10 36 36 HOH HOH . J 6 HOH B 11 37 37 HOH HOH . J 6 HOH B 12 38 38 HOH HOH . J 6 HOH B 13 39 39 HOH HOH . J 6 HOH B 14 40 40 HOH HOH . J 6 HOH B 15 41 41 HOH HOH . J 6 HOH B 16 42 42 HOH HOH . J 6 HOH B 17 43 43 HOH HOH . J 6 HOH B 18 44 44 HOH HOH . J 6 HOH B 19 45 45 HOH HOH . J 6 HOH B 20 46 46 HOH HOH . J 6 HOH B 21 47 47 HOH HOH . J 6 HOH B 22 48 48 HOH HOH . J 6 HOH B 23 49 49 HOH HOH . J 6 HOH B 24 50 50 HOH HOH . J 6 HOH B 25 51 51 HOH HOH . J 6 HOH B 26 52 52 HOH HOH . J 6 HOH B 27 53 53 HOH HOH . J 6 HOH B 28 54 54 HOH HOH . J 6 HOH B 29 55 55 HOH HOH . J 6 HOH B 30 56 56 HOH HOH . J 6 HOH B 31 57 57 HOH HOH . J 6 HOH B 32 58 58 HOH HOH . J 6 HOH B 33 59 59 HOH HOH . J 6 HOH B 34 60 60 HOH HOH . J 6 HOH B 35 61 61 HOH HOH . J 6 HOH B 36 62 62 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 . . . D 4 33.408 -3.466 18.304 1 41.51 ? PG GNP 200 A 1 HETATM 2 O O1G GNP . . . D 4 32.387 -4.261 19.071 1 48.25 ? O1G GNP 200 A 1 HETATM 3 O O2G GNP . . . D 4 34.845 -3.408 18.839 1 48.29 ? O2G GNP 200 A 1 HETATM 4 O O3G GNP . . . D 4 32.742 -2.133 18.057 1 40.58 ? O3G GNP 200 A 1 HETATM 5 N N3B GNP . . . D 4 33.626 -4.173 16.85 1 52.99 ? N3B GNP 200 A 1 HETATM 6 P PB GNP . . . D 4 34.57 -3.59 15.66 1 44.19 ? PB GNP 200 A 1 HETATM 7 O O1B GNP . . . D 4 33.81 -2.585 14.867 1 41.6 ? O1B GNP 200 A 1 HETATM 8 O O2B GNP . . . D 4 35.804 -3.219 16.408 1 43.72 ? O2B GNP 200 A 1 HETATM 9 O O3A GNP . . . D 4 34.957 -4.699 14.654 1 41.75 ? O3A GNP 200 A 1 HETATM 10 P PA GNP . . . D 4 36.224 -5.583 14.744 1 48.36 ? PA GNP 200 A 1 HETATM 11 O O1A GNP . . . D 4 37.325 -4.75 14.217 1 44.38 ? O1A GNP 200 A 1 HETATM 12 O O2A GNP . . . D 4 36.435 -6.23 16.087 1 45.55 ? O2A GNP 200 A 1 HETATM 13 O O5' GNP . . . D 4 35.98 -6.78 13.744 1 47.55 ? O5' GNP 200 A 1 HETATM 14 C C5' GNP . . . D 4 34.802 -7.52 13.815 1 44.77 ? C5' GNP 200 A 1 HETATM 15 C C4' GNP . . . D 4 35.067 -8.908 13.235 1 55.45 ? C4' GNP 200 A 1 HETATM 16 O O4' GNP . . . D 4 35.075 -8.895 11.793 1 49.11 ? O4' GNP 200 A 1 HETATM 17 C C3' GNP . . . D 4 36.374 -9.579 13.642 1 54.22 ? C3' GNP 200 A 1 HETATM 18 O O3' GNP . . . D 4 36.122 -10.966 13.743 1 61.11 ? O3' GNP 200 A 1 HETATM 19 C C2' GNP . . . D 4 37.315 -9.319 12.473 1 55.39 ? C2' GNP 200 A 1 HETATM 20 O O2' GNP . . . D 4 38.274 -10.352 12.278 1 55.64 ? O2' GNP 200 A 1 HETATM 21 C C1' GNP . . . D 4 36.356 -9.286 11.299 1 54.28 ? C1' GNP 200 A 1 HETATM 22 N N9 GNP . . . D 4 36.724 -8.326 10.258 1 55.24 ? N9 GNP 200 A 1 HETATM 23 C C8 GNP . . . D 4 37.042 -6.989 10.418 1 59.47 ? C8 GNP 200 A 1 HETATM 24 N N7 GNP . . . D 4 37.294 -6.367 9.294 1 50.37 ? N7 GNP 200 A 1 HETATM 25 C C5 GNP . . . D 4 37.134 -7.355 8.328 1 57.82 ? C5 GNP 200 A 1 HETATM 26 C C6 GNP . . . D 4 37.287 -7.274 6.908 1 56.15 ? C6 GNP 200 A 1 HETATM 27 O O6 GNP . . . D 4 37.607 -6.279 6.236 1 50.39 ? O6 GNP 200 A 1 HETATM 28 N N1 GNP . . . D 4 37.016 -8.499 6.287 1 56.18 ? N1 GNP 200 A 1 HETATM 29 C C2 GNP . . . D 4 36.66 -9.653 6.961 1 58.92 ? C2 GNP 200 A 1 HETATM 30 N N2 GNP . . . D 4 36.442 -10.733 6.214 1 64.46 ? N2 GNP 200 A 1 HETATM 31 N N3 GNP . . . D 4 36.523 -9.744 8.286 1 61.19 ? N3 GNP 200 A 1 HETATM 32 C C4 GNP . . . D 4 36.772 -8.56 8.908 1 57.55 ? C4 GNP 200 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 32 #