data_8E8B # _model_server_result.job_id m8696AaNZTOfOxRhFizLrQ _model_server_result.datetime_utc '2024-12-26 15:23:16' _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 8e8b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 8E8B # _exptl.entry_id 8E8B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _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 8E8B _cell.length_a 97.87 _cell.length_b 97.87 _cell.length_c 82.13 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8E8B _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,I _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 OD1 ASP 16 A ASP 13 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc2 A O MET 17 A MET 14 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc3 A OG SER 116 A SER 113 1_555 E K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.201 ? metalc ? metalc4 A OD1 ASP 118 A ASP 115 1_555 E K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc5 A OD2 ASP 118 A ASP 115 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc6 A OE1 GLU 119 A GLU 116 1_555 E K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc7 D O1A DGT . A DGT 501 1_555 E K K . A K 502 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.698 ? metalc ? metalc8 D O2G DGT . A DGT 501 1_555 F CA CA . A CA 503 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc9 D O2B DGT . A DGT 501 1_555 F CA CA . A CA 503 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc10 D O1A DGT . A DGT 501 1_555 F CA CA . A CA 503 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc11 E K K . A K 502 1_555 G O HOH . A HOH 625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc12 E K K . A K 502 1_555 C O3' U 8 P U 9 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.131 ? 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 N6 DA 5 T DA 6 1_555 C O4 U 8 P U 9 1_555 ? B ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N3 DT 6 T DT 7 1_555 C N1 DA 7 P DA 8 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DT 6 T DT 7 1_555 C N1 DA 7 P DA 8 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 DT 6 T DT 7 1_555 C N6 DA 7 P DA 8 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O4 DT 6 T DT 7 1_555 C N6 DA 7 P DA 8 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DG 7 T DG 8 1_555 C N3 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DG 7 T DG 8 1_555 C N3 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N2 DG 7 T DG 8 1_555 C O2 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N2 DG 7 T DG 8 1_555 C O2 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O6 DG 7 T DG 8 1_555 C N4 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 DG 7 T DG 8 1_555 C N4 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 DA 8 T DA 9 1_555 C N3 DT 5 P DT 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DA 8 T DA 9 1_555 C N3 DT 5 P DT 6 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N6 DA 8 T DA 9 1_555 C O4 DT 5 P DT 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N6 DA 8 T DA 9 1_555 C O4 DT 5 P DT 6 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DC 9 T DC 10 1_555 C N1 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N4 DC 9 T DC 10 1_555 C O6 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O2 DC 9 T DC 10 1_555 C N2 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 DG 10 T DG 11 1_555 C N3 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N2 DG 10 T DG 11 1_555 C O2 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O6 DG 10 T DG 11 1_555 C N4 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N3 DC 11 T DC 12 1_555 C N1 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N4 DC 11 T DC 12 1_555 C O6 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B O2 DC 11 T DC 12 1_555 C N2 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N3 DT 12 T DT 13 1_555 C N1 DA 1 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 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 8E8B _atom_sites.fract_transf_matrix[1][1] 0.010218 _atom_sites.fract_transf_matrix[1][2] 0.005899 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011798 _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] 0.012176 _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 DGT A 1 501 504 DGT DGT . E 5 K A 1 502 1 K K . F 6 CA A 1 503 1 CA CA . G 7 HOH A 1 601 25 HOH HOH . G 7 HOH A 2 602 24 HOH HOH . G 7 HOH A 3 603 23 HOH HOH . G 7 HOH A 4 604 4 HOH HOH . G 7 HOH A 5 605 10 HOH HOH . G 7 HOH A 6 606 13 HOH HOH . G 7 HOH A 7 607 38 HOH HOH . G 7 HOH A 8 608 6 HOH HOH . G 7 HOH A 9 609 32 HOH HOH . G 7 HOH A 10 610 3 HOH HOH . G 7 HOH A 11 611 11 HOH HOH . G 7 HOH A 12 612 34 HOH HOH . G 7 HOH A 13 613 12 HOH HOH . G 7 HOH A 14 614 37 HOH HOH . G 7 HOH A 15 615 40 HOH HOH . G 7 HOH A 16 616 28 HOH HOH . G 7 HOH A 17 617 15 HOH HOH . G 7 HOH A 18 618 5 HOH HOH . G 7 HOH A 19 619 22 HOH HOH . G 7 HOH A 20 620 30 HOH HOH . G 7 HOH A 21 621 29 HOH HOH . G 7 HOH A 22 622 9 HOH HOH . G 7 HOH A 23 623 21 HOH HOH . G 7 HOH A 24 624 20 HOH HOH . G 7 HOH A 25 625 1 HOH HOH . G 7 HOH A 26 626 26 HOH HOH . G 7 HOH A 27 627 16 HOH HOH . G 7 HOH A 28 628 2 HOH HOH . G 7 HOH A 29 629 14 HOH HOH . G 7 HOH A 30 630 7 HOH HOH . G 7 HOH A 31 631 18 HOH HOH . G 7 HOH A 32 632 39 HOH HOH . G 7 HOH A 33 633 17 HOH HOH . G 7 HOH A 34 634 31 HOH HOH . G 7 HOH A 35 635 27 HOH HOH . G 7 HOH A 36 636 36 HOH HOH . G 7 HOH A 37 637 33 HOH HOH . H 7 HOH T 1 101 19 HOH HOH . H 7 HOH T 2 102 35 HOH HOH . I 7 HOH P 1 101 8 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 . D 4 -19.439 38.837 8.166 0.9 52.03 ? PG DGT 501 A 1 HETATM 2 O O1G DGT . A . D 4 -18.069 38.159 8.228 0.9 49.31 ? O1G DGT 501 A 1 HETATM 3 O O2G DGT . A . D 4 -20.046 38.543 6.8 0.9 43.11 -1 O2G DGT 501 A 1 HETATM 4 O O3G DGT . A . D 4 -20.349 38.454 9.331 0.9 50.56 ? O3G DGT 501 A 1 HETATM 5 O O3B DGT . A . D 4 -19.11 40.408 8.124 0.9 50.96 ? O3B DGT 501 A 1 HETATM 6 P PB DGT . A . D 4 -19.165 41.53 6.991 0.9 65.35 ? PB DGT 501 A 1 HETATM 7 O O1B DGT . A . D 4 -18.436 42.775 7.486 0.9 42.38 -1 O1B DGT 501 A 1 HETATM 8 O O2B DGT . A . D 4 -18.655 41.079 5.665 0.9 37.06 ? O2B DGT 501 A 1 HETATM 9 O O3A DGT . A . D 4 -20.713 41.895 6.988 0.9 58.73 ? O3A DGT 501 A 1 HETATM 10 P PA DGT . A . D 4 -21.794 41.922 5.824 0.9 54.24 ? PA DGT 501 A 1 HETATM 11 O O1A DGT . A . D 4 -21.44 40.761 4.902 0.9 57.86 -1 O1A DGT 501 A 1 HETATM 12 O O2A DGT . A . D 4 -23.167 41.77 6.401 0.9 51.84 ? O2A DGT 501 A 1 HETATM 13 O O5' DGT . A . D 4 -21.481 43.259 4.961 0.9 52.38 ? O5' DGT 501 A 1 HETATM 14 C C5' DGT . A . D 4 -20.423 43.298 3.975 0.9 47.03 ? C5' DGT 501 A 1 HETATM 15 C C4' DGT . A . D 4 -19.597 44.558 4.055 0.9 45.07 ? C4' DGT 501 A 1 HETATM 16 O O4' DGT . A . D 4 -20.412 45.682 3.654 0.9 48.91 ? O4' DGT 501 A 1 HETATM 17 C C3' DGT . A . D 4 -19.051 44.905 5.441 0.9 50.17 ? C3' DGT 501 A 1 HETATM 18 O O3' DGT . A . D 4 -17.721 44.418 5.625 0.9 28.33 ? O3' DGT 501 A 1 HETATM 19 C C2' DGT . A . D 4 -19.011 46.428 5.419 0.9 32.68 ? C2' DGT 501 A 1 HETATM 20 C C1' DGT . A . D 4 -20.134 46.815 4.465 0.9 48.03 ? C1' DGT 501 A 1 HETATM 21 N N9 DGT . A . D 4 -21.381 47.216 5.137 0.9 45.11 ? N9 DGT 501 A 1 HETATM 22 C C8 DGT . A . D 4 -22.275 46.443 5.829 0.9 46.14 ? C8 DGT 501 A 1 HETATM 23 N N7 DGT . A . D 4 -23.293 47.158 6.322 0.9 47.31 ? N7 DGT 501 A 1 HETATM 24 C C5 DGT . A . D 4 -23.012 48.456 5.928 0.9 36.59 ? C5 DGT 501 A 1 HETATM 25 C C6 DGT . A . D 4 -23.641 49.704 6.21 0.9 49.84 ? C6 DGT 501 A 1 HETATM 26 O O6 DGT . A . D 4 -24.673 49.781 6.884 0.9 42.94 ? O6 DGT 501 A 1 HETATM 27 N N1 DGT . A . D 4 -23.081 50.839 5.755 0.9 51.39 ? N1 DGT 501 A 1 HETATM 28 C C2 DGT . A . D 4 -21.908 50.725 5.023 0.9 57.8 ? C2 DGT 501 A 1 HETATM 29 N N2 DGT . A . D 4 -21.357 51.878 4.626 0.9 41.18 ? N2 DGT 501 A 1 HETATM 30 N N3 DGT . A . D 4 -21.28 49.589 4.716 0.9 48.93 ? N3 DGT 501 A 1 HETATM 31 C C4 DGT . A . D 4 -21.864 48.5 5.201 0.9 50.14 ? C4 DGT 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #