data_3S8A # _model_server_result.job_id QCfKgHWlZWJEj4ia5-WnLQ _model_server_result.datetime_utc '2024-12-03 20:45:54' _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 3s8a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 3S8A # _exptl.entry_id 3S8A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _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 90 _cell.entry_id 3S8A _cell.length_a 108.443 _cell.length_b 117.716 _cell.length_c 64.781 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S8A _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 117.716 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 C O1G DGT . A DGT 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc2 C O1A DGT . A DGT 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc3 C O1B DGT . A DGT 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? # _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 83 n n PG O2G DGT sing 84 n n O1G HO1G DGT sing 85 n n O2G HO2G DGT sing 86 n n O3G PG DGT doub 87 n n O3B PG DGT sing 88 n n PB O3B DGT sing 89 n n PB O1B DGT sing 90 n n PB O3A DGT sing 91 n n O1B HO1B DGT sing 92 n n O2B PB DGT doub 93 n n PA O3A DGT sing 94 n n PA O1A DGT sing 95 n n O1A HO1A DGT sing 96 n n O2A PA DGT doub 97 n n O5' PA DGT sing 98 n n O5' C5' DGT sing 99 n n C5' H5' DGT sing 100 n n C5' "H5'A" DGT sing 101 n n C4' C5' DGT sing 102 n n C4' H4' DGT sing 103 n n O4' C4' DGT sing 104 n n C3' C4' DGT sing 105 n n C3' O3' DGT sing 106 n n C3' H3' DGT sing 107 n n O3' HO3' DGT sing 108 n n C2' C3' DGT sing 109 n n C2' C1' DGT sing 110 n n C2' H2' DGT sing 111 n n C2' "H2'A" DGT sing 112 n n C1' O4' DGT sing 113 n n C1' H1' DGT sing 114 n n N9 C1' DGT sing 115 n n N9 C4 DGT sing 116 n y C8 N9 DGT sing 117 n y C8 H8 DGT sing 118 n n N7 C8 DGT doub 119 n y N7 C5 DGT sing 120 n y C5 C6 DGT sing 121 n n C5 C4 DGT doub 122 n y C6 N1 DGT sing 123 n n O6 C6 DGT doub 124 n n N1 C2 DGT sing 125 n n C2 N3 DGT doub 126 n n C2 N2 DGT sing 127 n n N2 HN2 DGT sing 128 n n N2 HN2A DGT sing 129 n n C4 N3 DGT sing 130 n n N1 H16 DGT sing 131 n n # _atom_sites.entry_id 3S8A _atom_sites.fract_transf_matrix[1][1] 0.009221 _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] 0.008495 _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] 0.015437 _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 MG A 1 2001 2001 MG MG . C 3 DGT A 1 1001 1001 DGT DGT . D 4 HOH A 1 889 1 HOH HOH . D 4 HOH A 2 890 2 HOH HOH . D 4 HOH A 3 891 3 HOH HOH . D 4 HOH A 4 892 4 HOH HOH . D 4 HOH A 5 893 5 HOH HOH . D 4 HOH A 6 894 6 HOH HOH . D 4 HOH A 7 895 7 HOH HOH . D 4 HOH A 8 896 8 HOH HOH . D 4 HOH A 9 897 9 HOH HOH . D 4 HOH A 10 898 10 HOH HOH . D 4 HOH A 11 899 11 HOH HOH . D 4 HOH A 12 900 12 HOH HOH . D 4 HOH A 13 901 14 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 . . . C 3 -12.477 44.95 26.654 1 49.79 ? PG DGT 1001 A 1 HETATM 2 O O1G DGT . . . C 3 -10.943 45.128 26.891 1 46.84 ? O1G DGT 1001 A 1 HETATM 3 O O2G DGT . . . C 3 -13.215 44.698 28.01 1 49.33 ? O2G DGT 1001 A 1 HETATM 4 O O3G DGT . . . C 3 -12.942 44.186 25.361 1 42.66 ? O3G DGT 1001 A 1 HETATM 5 O O3B DGT . . . C 3 -13.018 46.434 26.222 1 49.82 ? O3B DGT 1001 A 1 HETATM 6 P PB DGT . . . C 3 -12.361 47.842 26.714 1 45.78 ? PB DGT 1001 A 1 HETATM 7 O O1B DGT . . . C 3 -11.624 47.822 28.066 1 47.45 ? O1B DGT 1001 A 1 HETATM 8 O O2B DGT . . . C 3 -13.521 48.814 26.491 1 47.41 ? O2B DGT 1001 A 1 HETATM 9 O O3A DGT . . . C 3 -11.316 47.905 25.466 1 48.35 ? O3A DGT 1001 A 1 HETATM 10 P PA DGT . . . C 3 -9.782 48.337 25.741 1 48.12 ? PA DGT 1001 A 1 HETATM 11 O O1A DGT . . . C 3 -9.181 47.471 26.866 1 45.69 ? O1A DGT 1001 A 1 HETATM 12 O O2A DGT . . . C 3 -9.692 49.858 25.974 1 52.27 ? O2A DGT 1001 A 1 HETATM 13 O O5' DGT . . . C 3 -9.267 48.083 24.202 1 44.09 ? O5' DGT 1001 A 1 HETATM 14 C C5' DGT . . . C 3 -9.087 46.697 24.013 1 43.41 ? C5' DGT 1001 A 1 HETATM 15 C C4' DGT . . . C 3 -8.6 46.508 22.611 1 44.41 ? C4' DGT 1001 A 1 HETATM 16 O O4' DGT . . . C 3 -9.545 47.126 21.743 1 44.02 ? O4' DGT 1001 A 1 HETATM 17 C C3' DGT . . . C 3 -7.275 47.211 22.403 1 44.78 ? C3' DGT 1001 A 1 HETATM 18 O O3' DGT . . . C 3 -6.246 46.23 22.116 1 40.04 ? O3' DGT 1001 A 1 HETATM 19 C C2' DGT . . . C 3 -7.534 48.152 21.221 1 44.75 ? C2' DGT 1001 A 1 HETATM 20 C C1' DGT . . . C 3 -8.924 47.862 20.704 1 42.62 ? C1' DGT 1001 A 1 HETATM 21 N N9 DGT . . . C 3 -9.794 49.063 20.557 1 43.35 ? N9 DGT 1001 A 1 HETATM 22 C C8 DGT . . . C 3 -10.573 49.618 21.554 1 43.69 ? C8 DGT 1001 A 1 HETATM 23 N N7 DGT . . . C 3 -11.297 50.687 21.017 1 43.32 ? N7 DGT 1001 A 1 HETATM 24 C C5 DGT . . . C 3 -10.984 50.8 19.686 1 42.23 ? C5 DGT 1001 A 1 HETATM 25 C C6 DGT . . . C 3 -11.368 51.704 18.562 1 42.77 ? C6 DGT 1001 A 1 HETATM 26 O O6 DGT . . . C 3 -12.183 52.663 18.737 1 42.51 ? O6 DGT 1001 A 1 HETATM 27 N N1 DGT . . . C 3 -10.826 51.468 17.342 1 43.37 ? N1 DGT 1001 A 1 HETATM 28 C C2 DGT . . . C 3 -9.935 50.455 17.111 1 43.83 ? C2 DGT 1001 A 1 HETATM 29 N N2 DGT . . . C 3 -9.432 50.294 15.819 1 42.72 ? N2 DGT 1001 A 1 HETATM 30 N N3 DGT . . . C 3 -9.532 49.596 18.128 1 42.01 ? N3 DGT 1001 A 1 HETATM 31 C C4 DGT . . . C 3 -10.007 49.722 19.39 1 41.63 ? C4 DGT 1001 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 215 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #