data_5AO0 # _model_server_result.job_id IUDsJfAX2ttZQMjqDfPKFw _model_server_result.datetime_utc '2025-02-17 06:20:39' _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 5ao0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2001}' # _entry.id 5AO0 # _exptl.entry_id 5AO0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 5AO0 _cell.length_a 163.173 _cell.length_b 163.173 _cell.length_c 260.716 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AO0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 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,L _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' 12_555 -x+2/3,-x+y+1/3,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 81.5865 47.103988 86.905333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 H N N ? 3 I N 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 disulf ? disulf1 A SG CYS 323 A CYS 341 1_555 A SG CYS 332 A CYS 350 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 B SG CYS 323 B CYS 341 1_555 B SG CYS 332 B CYS 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc1 A NE2 HIS 149 A HIS 167 1_555 C FE FE . A FE 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc2 A NE2 HIS 188 A HIS 206 1_555 C FE FE . A FE 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc3 A OD2 ASP 189 A ASP 207 1_555 C FE FE . A FE 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc4 A OD1 ASP 293 A ASP 311 1_555 C FE FE . A FE 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc5 C FE FE . A FE 1001 1_555 D O1B DG3 . A DG3 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc6 C FE FE . A FE 1001 1_555 D O3G DG3 . A DG3 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc7 E O2B DG3 . A DG3 2002 1_555 F MG MG . A MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc8 E O1B DG3 . A DG3 2002 1_555 F MG MG . A MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc9 B NE2 HIS 149 B HIS 167 1_555 G FE FE . B FE 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc10 B NE2 HIS 188 B HIS 206 1_555 G FE FE . B FE 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc11 B OD2 ASP 189 B ASP 207 1_555 G FE FE . B FE 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc12 B OD1 ASP 293 B ASP 311 1_555 G FE FE . B FE 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc13 G FE FE . B FE 1001 1_555 H O2G DG3 . B DG3 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc14 G FE FE . B FE 1001 1_555 H O1B DG3 . B DG3 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc15 I O2G DG3 . B DG3 2002 1_555 J MG MG . B MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? # _chem_comp.formula 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id DG3 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-3'-DIDEOXYGUANOSINE-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 DG3 doub 83 n n PG O2G DG3 sing 84 n n PG O3G DG3 sing 85 n n PG O3B DG3 sing 86 n n O2G HOG2 DG3 sing 87 n n O3G HOG3 DG3 sing 88 n n O3B PB DG3 sing 89 n n PB O1B DG3 doub 90 n n PB O2B DG3 sing 91 n n PB O3A DG3 sing 92 n n O2B HOB2 DG3 sing 93 n n O3A PA DG3 sing 94 n n PA O1A DG3 doub 95 n n PA O2A DG3 sing 96 n n PA O5' DG3 sing 97 n n O2A HOA2 DG3 sing 98 n n O5' C5' DG3 sing 99 n n C5' C4' DG3 sing 100 n n C5' "H5'1" DG3 sing 101 n n C5' "H5'2" DG3 sing 102 n n C4' O4' DG3 sing 103 n n C4' C3' DG3 sing 104 n n C4' H4' DG3 sing 105 n n O4' C1' DG3 sing 106 n n C3' C2' DG3 sing 107 n n C3' "H3'1" DG3 sing 108 n n C3' "H3'2" DG3 sing 109 n n C2' C1' DG3 sing 110 n n C2' "H2'1" DG3 sing 111 n n C2' "H2'2" DG3 sing 112 n n C1' N9 DG3 sing 113 n n C1' H1' DG3 sing 114 n n N9 C8 DG3 sing 115 n y N9 C4 DG3 sing 116 n y C8 N7 DG3 doub 117 n y C8 H8 DG3 sing 118 n n N7 C5 DG3 sing 119 n y C5 C6 DG3 sing 120 n n C5 C4 DG3 doub 121 n y C6 O6 DG3 doub 122 n n C6 N1 DG3 sing 123 n n N1 C2 DG3 sing 124 n n N1 HN1 DG3 sing 125 n n C2 N2 DG3 sing 126 n n C2 N3 DG3 doub 127 n n N2 HN21 DG3 sing 128 n n N2 HN22 DG3 sing 129 n n N3 C4 DG3 sing 130 n n # _atom_sites.entry_id 5AO0 _atom_sites.fract_transf_matrix[1][1] 0.006128 _atom_sites.fract_transf_matrix[1][2] 0.003538 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007077 _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] 0.003836 _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 2 FE A 1 1001 1001 FE FE . D 3 DG3 A 1 2001 2001 DG3 DG3 . E 3 DG3 A 1 2002 2002 DG3 DG3 . F 4 MG A 1 3001 3001 MG MG . G 2 FE B 1 1001 1001 FE FE . H 3 DG3 B 1 2001 2001 DG3 DG3 . I 3 DG3 B 1 2002 2002 DG3 DG3 . J 4 MG B 1 3001 3001 MG MG . K 5 HOH A 1 4001 4001 HOH HOH . K 5 HOH A 2 4002 4002 HOH HOH . L 5 HOH B 1 4001 4001 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 DG3 . . . D 3 46.847 41.559 22.788 1 127.57 ? PG DG3 2001 A 1 HETATM 2 O O1G DG3 . . . D 3 48.003 42.37 23.317 1 127.21 ? O1G DG3 2001 A 1 HETATM 3 O O2G DG3 . . . D 3 46.435 42.111 21.448 1 124.95 ? O2G DG3 2001 A 1 HETATM 4 O O3G DG3 . . . D 3 45.682 41.673 23.74 1 130.1 ? O3G DG3 2001 A 1 HETATM 5 O O3B DG3 . . . D 3 47.247 40.051 22.652 1 69.33 ? O3B DG3 2001 A 1 HETATM 6 P PB DG3 . . . D 3 47.232 39.022 23.858 1 72.33 ? PB DG3 2001 A 1 HETATM 7 O O1B DG3 . . . D 3 45.82 38.871 24.358 1 70.33 ? O1B DG3 2001 A 1 HETATM 8 O O2B DG3 . . . D 3 47.734 37.675 23.393 1 74.27 ? O2B DG3 2001 A 1 HETATM 9 O O3A DG3 . . . D 3 48.145 39.534 25.033 1 188.62 ? O3A DG3 2001 A 1 HETATM 10 P PA DG3 . . . D 3 49.717 39.693 24.951 1 91.14 ? PA DG3 2001 A 1 HETATM 11 O O1A DG3 . . . D 3 50.243 40.086 26.309 1 91.32 ? O1A DG3 2001 A 1 HETATM 12 O O2A DG3 . . . D 3 50.089 40.76 23.949 1 88.32 ? O2A DG3 2001 A 1 HETATM 13 O O5' DG3 . . . D 3 50.378 38.317 24.499 1 105.74 ? O5' DG3 2001 A 1 HETATM 14 C C5' DG3 . . . D 3 50.292 37.202 25.354 1 108.03 ? C5' DG3 2001 A 1 HETATM 15 C C4' DG3 . . . D 3 51.693 36.671 25.608 1 111.52 ? C4' DG3 2001 A 1 HETATM 16 O O4' DG3 . . . D 3 52.217 36.106 24.408 1 112.16 ? O4' DG3 2001 A 1 HETATM 17 C C3' DG3 . . . D 3 52.582 37.795 26.057 1 113.35 ? C3' DG3 2001 A 1 HETATM 18 C C2' DG3 . . . D 3 53.85 37.594 25.221 1 114.41 ? C2' DG3 2001 A 1 HETATM 19 C C1' DG3 . . . D 3 53.587 36.35 24.425 1 114.15 ? C1' DG3 2001 A 1 HETATM 20 N N9 DG3 . . . D 3 54.07 36.528 23.07 1 118.07 ? N9 DG3 2001 A 1 HETATM 21 C C8 DG3 . . . D 3 53.804 37.558 22.266 1 120.2 ? C8 DG3 2001 A 1 HETATM 22 N N7 DG3 . . . D 3 54.411 37.387 21.104 1 120.92 ? N7 DG3 2001 A 1 HETATM 23 C C5 DG3 . . . D 3 55.091 36.233 21.128 1 120.54 ? C5 DG3 2001 A 1 HETATM 24 C C6 DG3 . . . D 3 55.937 35.53 20.152 1 119.26 ? C6 DG3 2001 A 1 HETATM 25 O O6 DG3 . . . D 3 56.126 36.015 19.05 1 116.18 ? O6 DG3 2001 A 1 HETATM 26 N N1 DG3 . . . D 3 56.516 34.32 20.486 1 120.05 ? N1 DG3 2001 A 1 HETATM 27 C C2 DG3 . . . D 3 56.296 33.742 21.788 1 118.91 ? C2 DG3 2001 A 1 HETATM 28 N N2 DG3 . . . D 3 56.893 32.507 22.117 1 117.06 ? N2 DG3 2001 A 1 HETATM 29 N N3 DG3 . . . D 3 55.514 34.383 22.703 1 119.92 ? N3 DG3 2001 A 1 HETATM 30 C C4 DG3 . . . D 3 54.892 35.661 22.375 1 120.01 ? C4 DG3 2001 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 30 #