data_8E8D # _model_server_result.job_id ERuYbLZdY3rk84uBGs2TdA _model_server_result.datetime_utc '2024-11-13 12:17:27' _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 8e8d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":503}' # _entry.id 8E8D # _exptl.entry_id 8E8D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" _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 8E8D _cell.length_a 98.48 _cell.length_b 98.48 _cell.length_c 81.68 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8E8D _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 F _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 OD2 ASP 16 A ASP 13 1_555 D MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc2 A OD1 ASP 16 A ASP 13 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 D MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc4 A OD2 ASP 118 A ASP 115 1_555 D MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc5 A OD1 ASP 118 A ASP 115 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc6 A OE2 GLU 119 A GLU 116 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc7 D MN MN . A MN 501 1_555 F O2B DGT . A DGT 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.969 ? metalc ? metalc8 D MN MN . A MN 501 1_555 F O1A DGT . A DGT 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.403 ? metalc ? metalc9 D MN MN . A MN 501 1_555 F O2G DGT . A DGT 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.779 ? metalc ? metalc10 E MN MN . A MN 502 1_555 F O1A DGT . A DGT 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.972 ? metalc ? metalc11 E MN MN . A MN 502 1_555 G O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc12 E MN MN . A MN 502 1_555 C O3' U 8 P U 9 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.758 ? hydrog WATSON-CRICK hydrog1 B N1 DA 5 T DA 6 1_555 C N3 U 8 P U 9 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N1 DA 5 T DA 6 1_555 C N3 U 8 P U 9 1_555 ? B ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N6 DA 5 T DA 6 1_555 C O4 U 8 P U 9 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 6 T DT 7 1_555 C N1 DA 7 P DA 8 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N3 DT 6 T DT 7 1_555 C N1 DA 7 P DA 8 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O4 DT 6 T DT 7 1_555 C N6 DA 7 P DA 8 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 DT 6 T DT 7 1_555 C N6 DA 7 P DA 8 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DG 7 T DG 8 1_555 C N3 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DG 7 T DG 8 1_555 C N3 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N2 DG 7 T DG 8 1_555 C O2 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N2 DG 7 T DG 8 1_555 C O2 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O6 DG 7 T DG 8 1_555 C N4 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O6 DG 7 T DG 8 1_555 C N4 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 8 T DA 9 1_555 C N3 DT 5 P DT 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 DA 8 T DA 9 1_555 C N3 DT 5 P DT 6 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N6 DA 8 T DA 9 1_555 C O4 DT 5 P DT 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N6 DA 8 T DA 9 1_555 C O4 DT 5 P DT 6 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 DC 9 T DC 10 1_555 C N1 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N4 DC 9 T DC 10 1_555 C O6 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O2 DC 9 T DC 10 1_555 C N2 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N1 DG 10 T DG 11 1_555 C N3 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N2 DG 10 T DG 11 1_555 C O2 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O6 DG 10 T DG 11 1_555 C N4 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N3 DC 11 T DC 12 1_555 C N1 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N4 DC 11 T DC 12 1_555 C O6 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B O2 DC 11 T DC 12 1_555 C N2 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N3 DT 12 T DT 13 1_555 C N1 DA 1 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O4 DT 12 T DT 13 1_555 C N6 DA 1 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id DGT _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" _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 DGT sing 195 n n PG O2G DGT sing 196 n n O1G HO1G DGT sing 197 n n O2G HO2G DGT sing 198 n n O3G PG DGT doub 199 n n O3B PG DGT sing 200 n n PB O3B DGT sing 201 n n PB O1B DGT sing 202 n n PB O3A DGT sing 203 n n O1B HO1B DGT sing 204 n n O2B PB DGT doub 205 n n PA O3A DGT sing 206 n n PA O1A DGT sing 207 n n O1A HO1A DGT sing 208 n n O2A PA DGT doub 209 n n O5' PA DGT sing 210 n n O5' C5' DGT sing 211 n n C5' H5' DGT sing 212 n n C5' "H5'A" DGT sing 213 n n C4' C5' DGT sing 214 n n C4' H4' DGT sing 215 n n O4' C4' DGT sing 216 n n C3' C4' DGT sing 217 n n C3' O3' DGT sing 218 n n C3' H3' DGT sing 219 n n O3' HO3' DGT sing 220 n n C2' C3' DGT sing 221 n n C2' C1' DGT sing 222 n n C2' H2' DGT sing 223 n n C2' "H2'A" DGT sing 224 n n C1' O4' DGT sing 225 n n C1' H1' DGT sing 226 n n N9 C1' DGT sing 227 n n N9 C4 DGT sing 228 n y C8 N9 DGT sing 229 n y C8 H8 DGT sing 230 n n N7 C8 DGT doub 231 n y N7 C5 DGT sing 232 n y C5 C6 DGT sing 233 n n C5 C4 DGT doub 234 n y C6 N1 DGT sing 235 n n O6 C6 DGT doub 236 n n N1 C2 DGT sing 237 n n C2 N3 DGT doub 238 n n C2 N2 DGT sing 239 n n N2 HN2 DGT sing 240 n n N2 HN2A DGT sing 241 n n C4 N3 DGT sing 242 n n N1 H16 DGT sing 243 n n # _atom_sites.entry_id 8E8D _atom_sites.fract_transf_matrix[1][1] 0.010154 _atom_sites.fract_transf_matrix[1][2] 0.005863 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011725 _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] 0.012243 _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 D 4 MN A 1 501 502 MN MN . E 4 MN A 1 502 503 MN MN . F 5 DGT A 1 503 504 DGT DGT . G 6 HOH A 1 601 24 HOH HOH . G 6 HOH A 2 602 36 HOH HOH . G 6 HOH A 3 603 7 HOH HOH . G 6 HOH A 4 604 18 HOH HOH . G 6 HOH A 5 605 37 HOH HOH . G 6 HOH A 6 606 2 HOH HOH . G 6 HOH A 7 607 28 HOH HOH . G 6 HOH A 8 608 1 HOH HOH . G 6 HOH A 9 609 38 HOH HOH . G 6 HOH A 10 610 8 HOH HOH . G 6 HOH A 11 611 33 HOH HOH . G 6 HOH A 12 612 39 HOH HOH . G 6 HOH A 13 613 6 HOH HOH . G 6 HOH A 14 614 31 HOH HOH . G 6 HOH A 15 615 5 HOH HOH . G 6 HOH A 16 616 9 HOH HOH . G 6 HOH A 17 617 12 HOH HOH . G 6 HOH A 18 618 34 HOH HOH . G 6 HOH A 19 619 3 HOH HOH . G 6 HOH A 20 620 13 HOH HOH . G 6 HOH A 21 621 22 HOH HOH . G 6 HOH A 22 622 20 HOH HOH . G 6 HOH A 23 623 10 HOH HOH . G 6 HOH A 24 624 26 HOH HOH . G 6 HOH A 25 625 11 HOH HOH . G 6 HOH A 26 626 4 HOH HOH . G 6 HOH A 27 627 32 HOH HOH . G 6 HOH A 28 628 35 HOH HOH . G 6 HOH A 29 629 14 HOH HOH . G 6 HOH A 30 630 17 HOH HOH . G 6 HOH A 31 631 25 HOH HOH . G 6 HOH A 32 632 21 HOH HOH . G 6 HOH A 33 633 23 HOH HOH . G 6 HOH A 34 634 30 HOH HOH . G 6 HOH A 35 635 19 HOH HOH . G 6 HOH A 36 636 27 HOH HOH . G 6 HOH A 37 637 29 HOH HOH . G 6 HOH A 38 638 16 HOH HOH . H 6 HOH T 1 101 15 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 DGT . A . F 5 -19.354 38.936 7.925 0.8 40.65 ? PG DGT 503 A 1 HETATM 2 O O1G DGT . A . F 5 -18.067 38.161 8.097 0.8 43.61 ? O1G DGT 503 A 1 HETATM 3 O O2G DGT . A . F 5 -19.861 38.771 6.506 0.8 39.85 -1 O2G DGT 503 A 1 HETATM 4 O O3G DGT . A . F 5 -20.362 38.651 8.97 0.8 40.74 ? O3G DGT 503 A 1 HETATM 5 O O3B DGT . A . F 5 -18.914 40.458 7.997 0.8 40.39 ? O3B DGT 503 A 1 HETATM 6 P PB DGT . A . F 5 -19.192 41.58 6.91 0.8 43.93 ? PB DGT 503 A 1 HETATM 7 O O1B DGT . A . F 5 -18.621 42.889 7.454 0.8 32.85 -1 O1B DGT 503 A 1 HETATM 8 O O2B DGT . A . F 5 -18.747 41.202 5.551 0.8 31.83 ? O2B DGT 503 A 1 HETATM 9 O O3A DGT . A . F 5 -20.781 41.704 6.956 0.8 47.98 ? O3A DGT 503 A 1 HETATM 10 P PA DGT . A . F 5 -21.896 41.819 5.826 0.8 48.32 ? PA DGT 503 A 1 HETATM 11 O O1A DGT . A . F 5 -21.641 40.687 4.81 0.8 35.95 -1 O1A DGT 503 A 1 HETATM 12 O O2A DGT . A . F 5 -23.282 41.94 6.392 0.8 39.42 ? O2A DGT 503 A 1 HETATM 13 O O5' DGT . A . F 5 -21.495 43.176 5.087 0.8 53.22 ? O5' DGT 503 A 1 HETATM 14 C C5' DGT . A . F 5 -20.657 43.224 3.916 0.8 43.76 ? C5' DGT 503 A 1 HETATM 15 C C4' DGT . A . F 5 -19.741 44.42 3.938 0.8 39.97 ? C4' DGT 503 A 1 HETATM 16 O O4' DGT . A . F 5 -20.483 45.578 3.508 0.8 46.98 ? O4' DGT 503 A 1 HETATM 17 C C3' DGT . A . F 5 -19.159 44.771 5.304 0.8 34.3 ? C3' DGT 503 A 1 HETATM 18 O O3' DGT . A . F 5 -17.848 44.226 5.436 0.8 31.43 ? O3' DGT 503 A 1 HETATM 19 C C2' DGT . A . F 5 -19.062 46.287 5.259 0.8 34 ? C2' DGT 503 A 1 HETATM 20 C C1' DGT . A . F 5 -20.193 46.693 4.33 0.8 41.06 ? C1' DGT 503 A 1 HETATM 21 N N9 DGT . A . F 5 -21.425 47.078 5.024 0.8 37.52 ? N9 DGT 503 A 1 HETATM 22 C C8 DGT . A . F 5 -22.32 46.312 5.716 0.8 39.25 ? C8 DGT 503 A 1 HETATM 23 N N7 DGT . A . F 5 -23.333 47.031 6.194 0.8 45.04 ? N7 DGT 503 A 1 HETATM 24 C C5 DGT . A . F 5 -23.051 48.321 5.778 0.8 37.44 ? C5 DGT 503 A 1 HETATM 25 C C6 DGT . A . F 5 -23.716 49.538 5.973 0.8 51.92 ? C6 DGT 503 A 1 HETATM 26 O O6 DGT . A . F 5 -24.778 49.603 6.583 0.8 51.36 ? O6 DGT 503 A 1 HETATM 27 N N1 DGT . A . F 5 -23.191 50.663 5.47 0.8 45.36 ? N1 DGT 503 A 1 HETATM 28 C C2 DGT . A . F 5 -22.006 50.546 4.767 0.8 45.4 ? C2 DGT 503 A 1 HETATM 29 N N2 DGT . A . F 5 -21.507 51.688 4.291 0.8 39.32 ? N2 DGT 503 A 1 HETATM 30 N N3 DGT . A . F 5 -21.338 49.421 4.546 0.8 41.57 ? N3 DGT 503 A 1 HETATM 31 C C4 DGT . A . F 5 -21.903 48.356 5.074 0.8 45.71 ? C4 DGT 503 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #