data_5OG1 # _model_server_result.job_id gnz01jvyOY-YfYeYJaSMgw _model_server_result.datetime_utc '2024-10-20 20:17:29' _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 5og1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":901}' # _entry.id 5OG1 # _exptl.entry_id 5OG1 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,M _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 ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N # _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 5OG1 _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 G 2 AGS C 1 901 901 AGS AGS . H 2 AGS C 1 902 902 AGS AGS . I 2 AGS E 1 901 901 AGS AGS . J 2 AGS E 1 902 902 AGS AGS . K 2 AGS D 1 901 901 AGS AGS . L 2 AGS D 1 902 902 AGS AGS . M 2 AGS B 1 901 901 AGS AGS . # 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 . . . I 2 175.204 185.7 141.067 1 0 ? PG AGS 901 E 1 HETATM 2 S S1G AGS . . . I 2 174.961 184.061 142.093 1 0 ? S1G AGS 901 E 1 HETATM 3 O O2G AGS . . . I 2 174.401 185.65 139.738 1 0 ? O2G AGS 901 E 1 HETATM 4 O O3G AGS . . . I 2 174.742 186.922 141.911 1 0 ? O3G AGS 901 E 1 HETATM 5 P PB AGS . . . I 2 177.481 184.579 140.201 1 0 ? PB AGS 901 E 1 HETATM 6 O O1B AGS . . . I 2 176.43 183.482 140.016 1 0 ? O1B AGS 901 E 1 HETATM 7 O O2B AGS . . . I 2 178.507 184.201 141.194 1 0 ? O2B AGS 901 E 1 HETATM 8 O O3B AGS . . . I 2 176.702 185.858 140.698 1 0 ? O3B AGS 901 E 1 HETATM 9 P PA AGS . . . I 2 178.16 186.299 138.146 1 0 ? PA AGS 901 E 1 HETATM 10 O O1A AGS . . . I 2 177.901 186.286 136.69 1 0 ? O1A AGS 901 E 1 HETATM 11 O O2A AGS . . . I 2 177.178 187.179 138.927 1 0 ? O2A AGS 901 E 1 HETATM 12 O O3A AGS . . . I 2 178.122 184.836 138.772 1 0 ? O3A AGS 901 E 1 HETATM 13 O O5' AGS . . . I 2 179.649 186.813 138.334 1 0 ? O5' AGS 901 E 1 HETATM 14 C C5' AGS . . . I 2 179.978 187.777 139.356 1 0 ? C5' AGS 901 E 1 HETATM 15 C C4' AGS . . . I 2 180.308 189.116 138.737 1 0 ? C4' AGS 901 E 1 HETATM 16 O O4' AGS . . . I 2 181.721 189.383 138.896 1 0 ? O4' AGS 901 E 1 HETATM 17 C C3' AGS . . . I 2 180.022 189.262 137.244 1 0 ? C3' AGS 901 E 1 HETATM 18 O O3' AGS . . . I 2 178.723 189.796 137.023 1 0 ? O3' AGS 901 E 1 HETATM 19 C C2' AGS . . . I 2 181.114 190.227 136.791 1 0 ? C2' AGS 901 E 1 HETATM 20 O O2' AGS . . . I 2 180.791 191.577 137.102 1 0 ? O2' AGS 901 E 1 HETATM 21 C C1' AGS . . . I 2 182.288 189.772 137.659 1 0 ? C1' AGS 901 E 1 HETATM 22 N N9 AGS . . . I 2 183.136 188.657 137.199 1 0 ? N9 AGS 901 E 1 HETATM 23 C C8 AGS . . . I 2 183.971 188.002 138.059 1 0 ? C8 AGS 901 E 1 HETATM 24 N N7 AGS . . . I 2 184.666 187.04 137.506 1 0 ? N7 AGS 901 E 1 HETATM 25 C C5 AGS . . . I 2 184.249 187.05 136.186 1 0 ? C5 AGS 901 E 1 HETATM 26 C C6 AGS . . . I 2 184.612 186.261 135.072 1 0 ? C6 AGS 901 E 1 HETATM 27 N N6 AGS . . . I 2 185.497 185.262 135.12 1 0 ? N6 AGS 901 E 1 HETATM 28 N N1 AGS . . . I 2 184.018 186.532 133.889 1 0 ? N1 AGS 901 E 1 HETATM 29 C C2 AGS . . . I 2 183.128 187.524 133.829 1 0 ? C2 AGS 901 E 1 HETATM 30 N N3 AGS . . . I 2 182.715 188.333 134.807 1 0 ? N3 AGS 901 E 1 HETATM 31 C C4 AGS . . . I 2 183.311 188.045 135.972 1 0 ? C4 AGS 901 E 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 31 #