data_6OF3 # _model_server_result.job_id 8NFHYiHbmqt4B_7nCFfbAg _model_server_result.datetime_utc '2024-10-15 09:17:19' _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 6of3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":801}' # _entry.id 6OF3 # _exptl.entry_id 6OF3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 2 _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 6OF3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6OF3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G 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 metalc ? metalc1 B OG SER 167 B SER 275 1_555 F MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc2 E O3G AGS . B AGS 801 1_555 F MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc3 E O2B AGS . B AGS 801 1_555 F MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc4 D OG SER 167 E SER 275 1_555 H MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc5 G O3G AGS . E AGS 801 1_555 H MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc6 G O2B AGS . E AGS 801 1_555 H MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 6OF3 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 E 3 AGS B 1 801 801 AGS AGS . F 4 MG B 1 802 802 MG MG . G 3 AGS E 1 801 801 AGS AGS . H 4 MG E 1 802 802 MG MG . # 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 AGS . . . G 3 91.847 119.884 109.089 1 112.43 ? PG AGS 801 E 1 HETATM 2 S S1G AGS . . . G 3 91.021 121.187 110.264 1 112.43 ? S1G AGS 801 E 1 HETATM 3 O O2G AGS . . . G 3 93.347 119.976 109.134 1 112.43 ? O2G AGS 801 E 1 HETATM 4 O O3G AGS . . . G 3 91.4 118.498 109.461 1 112.43 ? O3G AGS 801 E 1 HETATM 5 P PB AGS . . . G 3 90.713 118.733 106.887 1 112.43 ? PB AGS 801 E 1 HETATM 6 O O1B AGS . . . G 3 91.881 117.892 106.448 1 112.43 ? O1B AGS 801 E 1 HETATM 7 O O2B AGS . . . G 3 89.671 118.123 107.787 1 112.43 ? O2B AGS 801 E 1 HETATM 8 O O3B AGS . . . G 3 91.308 120.043 107.592 1 112.43 ? O3B AGS 801 E 1 HETATM 9 P PA AGS . . . G 3 88.563 119.975 105.731 1 112.43 ? PA AGS 801 E 1 HETATM 10 O O1A AGS . . . G 3 87.513 118.95 105.404 1 112.43 ? O1A AGS 801 E 1 HETATM 11 O O2A AGS . . . G 3 88.551 120.655 107.072 1 112.43 ? O2A AGS 801 E 1 HETATM 12 O O3A AGS . . . G 3 89.999 119.287 105.564 1 112.43 ? O3A AGS 801 E 1 HETATM 13 O O5' AGS . . . G 3 88.533 121.092 104.589 1 112.43 ? O5' AGS 801 E 1 HETATM 14 C C5' AGS . . . G 3 89.683 121.844 104.229 1 112.43 ? C5' AGS 801 E 1 HETATM 15 C C4' AGS . . . G 3 89.254 122.739 103.104 1 112.43 ? C4' AGS 801 E 1 HETATM 16 O O4' AGS . . . G 3 89.211 121.989 101.87 1 112.43 ? O4' AGS 801 E 1 HETATM 17 C C3' AGS . . . G 3 87.87 123.341 103.279 1 112.43 ? C3' AGS 801 E 1 HETATM 18 O O3' AGS . . . G 3 87.942 124.739 103.47 1 112.43 ? O3' AGS 801 E 1 HETATM 19 C C2' AGS . . . G 3 87.085 122.943 102.035 1 112.43 ? C2' AGS 801 E 1 HETATM 20 O O2' AGS . . . G 3 86.46 124.086 101.477 1 112.43 ? O2' AGS 801 E 1 HETATM 21 C C1' AGS . . . G 3 88.176 122.498 101.068 1 112.43 ? C1' AGS 801 E 1 HETATM 22 N N9 AGS . . . G 3 87.773 121.457 100.102 1 112.43 ? N9 AGS 801 E 1 HETATM 23 C C8 AGS . . . G 3 88.407 120.261 99.912 1 112.43 ? C8 AGS 801 E 1 HETATM 24 N N7 AGS . . . G 3 87.859 119.503 99 1 112.43 ? N7 AGS 801 E 1 HETATM 25 C C5 AGS . . . G 3 86.783 120.251 98.559 1 112.43 ? C5 AGS 801 E 1 HETATM 26 C C6 AGS . . . G 3 85.797 120.002 97.59 1 112.43 ? C6 AGS 801 E 1 HETATM 27 N N6 AGS . . . G 3 85.735 118.885 96.865 1 112.43 ? N6 AGS 801 E 1 HETATM 28 N N1 AGS . . . G 3 84.858 120.945 97.378 1 112.43 ? N1 AGS 801 E 1 HETATM 29 C C2 AGS . . . G 3 84.915 122.066 98.098 1 112.43 ? C2 AGS 801 E 1 HETATM 30 N N3 AGS . . . G 3 85.791 122.414 99.031 1 112.43 ? N3 AGS 801 E 1 HETATM 31 C C4 AGS . . . G 3 86.709 121.455 99.229 1 112.43 ? C4 AGS 801 E 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #