data_1GAG # _model_server_result.job_id O41I72S1NB5rhAAfOVTEAA _model_server_result.datetime_utc '2024-11-21 14:22:17' _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 1gag # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":101}' # _entry.id 1GAG # _exptl.entry_id 1GAG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 580.298 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'THIOPHOSPHORIC ACID O-((ADENOSYL-PHOSPHO)PHOSPHO)-S-ACETAMIDYL-DIESTER' _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 1GAG _cell.length_a 66.3 _cell.length_b 66.3 _cell.length_c 138.1 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GAG _symmetry.cell_setting trigonal _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 2 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' 4_465 y-1,x+1,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 -99.45 57.417484 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 covale ? covale1 A C ILE 180 A ILE 1157 1_555 A N PTR 181 A PTR 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C PTR 181 A PTR 1158 1_555 A N GLU 182 A GLU 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C ASP 184 A ASP 1161 1_555 A N PTR 185 A PTR 1162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale4 A C PTR 185 A PTR 1162 1_555 A N PTR 186 A PTR 1163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 A C PTR 186 A PTR 1163 1_555 A N ARG 187 A ARG 1164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 E NS 112 . B 112 101 1_555 B CZ PHE 6 B PHE 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? metalc ? metalc1 F O HOH . A HOH 21 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.584 ? metalc ? metalc2 F O HOH . A HOH 22 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc3 C MG MG . A MG 201 1_555 A OD1 ASN 160 A ASN 1137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc4 C MG MG . A MG 201 1_555 A OD2 ASP 173 A ASP 1150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc5 C MG MG . A MG 201 1_555 G O HOH . B HOH 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc6 C MG MG . A MG 201 1_555 E O2S 112 . B 112 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc7 C MG MG . A MG 201 1_555 E O2G 112 . B 112 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc8 C MG MG . A MG 201 1_555 E O2B 112 . B 112 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? metalc ? metalc9 D MG MG . A MG 202 1_555 A OD2 ASP 173 A ASP 1150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.134 ? metalc ? metalc10 D MG MG . A MG 202 1_555 G O HOH . B HOH 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? # _chem_comp.formula 'C12 H19 N6 O13 P3 S' _chem_comp.formula_weight 580.298 _chem_comp.id 112 _chem_comp.mon_nstd_flag . _chem_comp.name 'THIOPHOSPHORIC ACID O-((ADENOSYL-PHOSPHO)PHOSPHO)-S-ACETAMIDYL-DIESTER' _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 NS C2S 112 sing 1 n n NS HNS1 112 sing 2 n n NS HNS2 112 sing 3 n n C2S O2S 112 doub 4 n n C2S C1S 112 sing 5 n n C1S S1G 112 sing 6 n n C1S H1S1 112 sing 7 n n C1S H1S2 112 sing 8 n n PG S1G 112 sing 9 n n PG O2G 112 sing 10 n n PG O3G 112 doub 11 n n PG O3B 112 sing 12 n n O2G HOG2 112 sing 13 n n PB O1B 112 doub 14 n n PB O2B 112 sing 15 n n PB O3B 112 sing 16 n n PB O3A 112 sing 17 n n O2B HOB2 112 sing 18 n n PA O1A 112 doub 19 n n PA O2A 112 sing 20 n n PA O3A 112 sing 21 n n PA O5' 112 sing 22 n n O2A HOA2 112 sing 23 n n O5' C5' 112 sing 24 n n C5' C4' 112 sing 25 n n C5' "H5'1" 112 sing 26 n n C5' "H5'2" 112 sing 27 n n C4' O4' 112 sing 28 n n C4' C3' 112 sing 29 n n C4' H4' 112 sing 30 n n O4' C1' 112 sing 31 n n C3' O3' 112 sing 32 n n C3' C2' 112 sing 33 n n C3' H3' 112 sing 34 n n O3' HO3' 112 sing 35 n n C2' O2' 112 sing 36 n n C2' C1' 112 sing 37 n n C2' H2' 112 sing 38 n n O2' HO2' 112 sing 39 n n C1' N9 112 sing 40 n n C1' H1' 112 sing 41 n n N9 C8 112 sing 42 n y N9 C4 112 sing 43 n y C8 N7 112 doub 44 n y C8 H8 112 sing 45 n n N7 C5 112 sing 46 n y C5 C6 112 sing 47 n y C5 C4 112 doub 48 n y C6 N6 112 sing 49 n n C6 N1 112 doub 50 n y N6 HN61 112 sing 51 n n N6 HN62 112 sing 52 n n N1 C2 112 sing 53 n y C2 N3 112 doub 54 n y C2 H2 112 sing 55 n n N3 C4 112 sing 56 n y # _atom_sites.entry_id 1GAG _atom_sites.fract_transf_matrix[1][1] 0.015083 _atom_sites.fract_transf_matrix[1][2] 0.008708 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017416 _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] 0.007241 _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 1 201 201 MG MG . D 3 MG A 1 202 202 MG MG . E 4 112 B 1 101 101 112 112 . F 5 HOH A 1 2 2 HOH HOH . F 5 HOH A 2 3 3 HOH HOH . F 5 HOH A 3 4 4 HOH HOH . F 5 HOH A 4 5 5 HOH HOH . F 5 HOH A 5 7 7 HOH HOH . F 5 HOH A 6 8 8 HOH HOH . F 5 HOH A 7 9 9 HOH HOH . F 5 HOH A 8 10 10 HOH HOH . F 5 HOH A 9 11 11 HOH HOH . F 5 HOH A 10 12 12 HOH HOH . F 5 HOH A 11 13 13 HOH HOH . F 5 HOH A 12 15 15 HOH HOH . F 5 HOH A 13 16 16 HOH HOH . F 5 HOH A 14 17 17 HOH HOH . F 5 HOH A 15 18 18 HOH HOH . F 5 HOH A 16 19 19 HOH HOH . F 5 HOH A 17 21 21 HOH HOH . F 5 HOH A 18 22 22 HOH HOH . F 5 HOH A 19 23 23 HOH HOH . G 5 HOH B 1 1 1 HOH HOH . G 5 HOH B 2 6 6 HOH HOH . G 5 HOH B 3 14 14 HOH HOH . G 5 HOH B 4 20 20 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 N NS 112 . . . E 4 -25.111 29.804 16.378 1 16.89 ? NS 112 101 B 1 HETATM 2 C C2S 112 . . . E 4 -25.076 29.463 15.09 1 17.97 ? C2S 112 101 B 1 HETATM 3 O O2S 112 . . . E 4 -25.149 30.392 14.279 1 17.83 ? O2S 112 101 B 1 HETATM 4 C C1S 112 . . . E 4 -24.949 28.023 14.594 1 16.45 ? C1S 112 101 B 1 HETATM 5 P PG 112 . . . E 4 -22.837 27.815 12.434 1 16.39 ? PG 112 101 B 1 HETATM 6 S S1G 112 . . . E 4 -23.252 27.403 14.369 1 18.36 ? S1G 112 101 B 1 HETATM 7 O O2G 112 . . . E 4 -22.925 29.264 12.188 1 16.9 ? O2G 112 101 B 1 HETATM 8 O O3G 112 . . . E 4 -21.569 27.195 11.995 1 16.48 ? O3G 112 101 B 1 HETATM 9 P PB 112 . . . E 4 -25.29 27.565 10.998 1 14.7 ? PB 112 101 B 1 HETATM 10 O O1B 112 . . . E 4 -26.313 26.538 11.298 1 12.35 ? O1B 112 101 B 1 HETATM 11 O O2B 112 . . . E 4 -25.578 28.965 11.334 1 15.7 ? O2B 112 101 B 1 HETATM 12 O O3B 112 . . . E 4 -23.887 27.202 11.502 1 16.49 ? O3B 112 101 B 1 HETATM 13 P PA 112 . . . E 4 -25.687 27.833 8.262 1 15.31 ? PA 112 101 B 1 HETATM 14 O O1A 112 . . . E 4 -26.645 26.711 8.061 1 14.38 ? O1A 112 101 B 1 HETATM 15 O O2A 112 . . . E 4 -26.171 29.242 8.328 1 14.69 ? O2A 112 101 B 1 HETATM 16 O O3A 112 . . . E 4 -24.902 27.506 9.525 1 15.45 ? O3A 112 101 B 1 HETATM 17 O O5' 112 . . . E 4 -24.545 27.79 7.092 1 15.09 ? O5' 112 101 B 1 HETATM 18 C C5' 112 . . . E 4 -23.275 27.09 7.208 1 13.98 ? C5' 112 101 B 1 HETATM 19 C C4' 112 . . . E 4 -22.104 27.659 6.44 1 13.41 ? C4' 112 101 B 1 HETATM 20 O O4' 112 . . . E 4 -22.481 27.806 5.043 1 14.43 ? O4' 112 101 B 1 HETATM 21 C C3' 112 . . . E 4 -21.652 29.054 6.848 1 14.67 ? C3' 112 101 B 1 HETATM 22 O O3' 112 . . . E 4 -20.753 29.024 7.955 1 15.23 ? O3' 112 101 B 1 HETATM 23 C C2' 112 . . . E 4 -20.948 29.537 5.589 1 15.07 ? C2' 112 101 B 1 HETATM 24 O O2' 112 . . . E 4 -19.646 28.995 5.48 1 17.03 ? O2' 112 101 B 1 HETATM 25 C C1' 112 . . . E 4 -21.844 28.951 4.49 1 14.99 ? C1' 112 101 B 1 HETATM 26 N N9 112 . . . E 4 -22.87 29.878 3.982 1 13.67 ? N9 112 101 B 1 HETATM 27 C C8 112 . . . E 4 -24.104 30.154 4.524 1 13.48 ? C8 112 101 B 1 HETATM 28 N N7 112 . . . E 4 -24.795 31.041 3.844 1 12.63 ? N7 112 101 B 1 HETATM 29 C C5 112 . . . E 4 -23.967 31.373 2.784 1 12.11 ? C5 112 101 B 1 HETATM 30 C C6 112 . . . E 4 -24.121 32.266 1.703 1 12.84 ? C6 112 101 B 1 HETATM 31 N N6 112 . . . E 4 -25.206 33.021 1.51 1 12.39 ? N6 112 101 B 1 HETATM 32 N N1 112 . . . E 4 -23.109 32.361 0.817 1 12.26 ? N1 112 101 B 1 HETATM 33 C C2 112 . . . E 4 -22.019 31.608 1.014 1 12.66 ? C2 112 101 B 1 HETATM 34 N N3 112 . . . E 4 -21.754 30.737 1.987 1 10.98 ? N3 112 101 B 1 HETATM 35 C C4 112 . . . E 4 -22.779 30.664 2.852 1 11.89 ? C4 112 101 B 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 43 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 1030 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 35 #